COMMISSION STAFF WORKING DOCUMENT Second River Basin Management Plans - Member State: Estonia Accompanying the document REPORT FROM THE COMMISSION TO THE EUROPEAN PARLIAMENT AND THE COUNCIL on the implementation of the Water Framework Directive (2000/60/EC) and the Floods Directive (2007/60/EC) Second River Basin Management Plans First Flood Risk Management Plans
Date: 2019-02-26
Institutions: Directorate-General for Environment, European Commission
Subjects: Estonia, adaptation to climate change, application of EU law, environmental risk prevention, flood, risk management, water, water management, water pollution, watercourse

EN 

  EN 

   EUROPEAN COMMISSION  Brussels, 26.2.2019  SWD(2019) 40 final  COMMISSION STAFF WORKING DOCUMENT Second River Basin Management Plans - Member State: Estonia Accompanying the document REPORT FROM THE COMMISSION TO THE EUROPEAN PARLIAMENT AND THE COUNCIL on the implementation of the Water Framework Directive (2000/60/EC) and the Floods Directive (2007/60/EC) Second River Basin Management Plans First Flood Risk Management Plans  {COM(2019) 95 final} - {SWD(2019) 30 final} - {SWD(2019) 31 final} - {SWD(2019) 32 final} - {SWD(2019) 33 final} - {SWD(2019) 34 final} - {SWD(2019) 35 final} - {SWD(2019) 36 final} - {SWD(2019) 37 final} - {SWD(2019) 38 final} - {SWD(2019) 39 final} - {SWD(2019) 41 final} - {SWD(2019) 42 final} - {SWD(2019) 43 final} - {SWD(2019) 44 final} - {SWD(2019) 45 final} - {SWD(2019) 46 final} - {SWD(2019) 47 final} - {SWD(2019) 48 final} - {SWD(2019) 49 final} - {SWD(2019) 50 final} - {SWD(2019) 51 final} - {SWD(2019) 52 final} - {SWD(2019) 53 final} - {SWD(2019) 54 final} - {SWD(2019) 55 final} - {SWD(2019) 56 final} - {SWD(2019) 57 final} - {SWD(2019) 58 final} - {SWD(2019) 59 final} - {SWD(2019) 60 final} - {SWD(2019) 61 final} - {SWD(2019) 62 final} - {SWD(2019) 63 final} - {SWD(2019) 64 final} - {SWD(2019) 65 final} - {SWD(2019) 66 final} - {SWD(2019) 67 final} - {SWD(2019) 68 final} - {SWD(2019) 69 final} - {SWD(2019) 70 final} - {SWD(2019) 71 final} - {SWD(2019) 72 final} - {SWD(2019) 73 final} - {SWD(2019) 74 final} - {SWD(2019) 75 final} - {SWD(2019) 76 final} - {SWD(2019) 77 final} - {SWD(2019) 78 final} - {SWD(2019) 79 final} - {SWD(2019) 80 final} - 
 
 
Table of contents 
Acronyms and definitions ............................................................................................................... 4 

Foreword ........................................................................................................................................ 5 

General Information ....................................................................................................................... 6 

Status of second river basin management plan reporting .............................................................. 8 

Key strengths, improvements and weaknesses of the second River Basin Management Plans ...... 9 

Recommendations ......................................................................................................................... 15 

Topic 1

  Governance and public participation .......................................................................... 18 

1.1

  Assessment of implementation and compliance with WFD requirements in second cycle 
 ......................................................................................................................................... 18 

1.2

  Main changes in implementation and compliance since first cycle ................................ 20 

1.3

  Progress with Commission recommendations ................................................................ 20 

Topic 2 Characterisation of the River Basin District ................................................................... 22 

2.1.  Assessment of implementation and compliance with the WFD requirements in the 
second cycle .............................................................................................................................. 22 

2.2.  Main changes in implementation and compliance since the first cycle .......................... 33 

2.3.  Progress with Commission recommendations ................................................................ 34 

Topic 3 Monitoring, assessment and classification of ecological status in surface water bodies 37 

3.1.  Assessment of implementation and compliance with WFD requirements in second 
RBMPs ...................................................................................................................................... 37 

3.2.  Main changes in implementation and compliance since first RBMPs ............................ 58 

3.3.  Progress with Commission recommendations ................................................................ 60 

Topic 4 Monitoring, assessment and classification of chemical status in surface water bodies . 62 

4.1.  Assessment of implementation and compliance with WFD requirements in second cycle 
 ......................................................................................................................................... 62 

4.2.  Main changes in implementation and compliance since first cycle ................................ 76 

4.3.  Progress with Commission recommendations ................................................................ 77 

Topic 5 Monitoring, assessment and classification of quantitative status of groundwater bodies
 ...................................................................................................................................................... 81 

5.1.  Assessment of implementation and compliance with the WFD requirements in the 
second cycle .............................................................................................................................. 81 

5.2.  Main changes in implementation and compliance since the first cycle .......................... 87 

5.3.  Progress with Commission recommendations ................................................................ 88 

Topic 6 Monitoring, assessment and classification of chemical status of groundwater bodies ... 90 

6.1.  Assessment of implementation and compliance with the WFD requirements in the 
second cycle .............................................................................................................................. 90 

1 

 
 
 
 
 
6.2.  Main changes in implementation and compliance since the first cycle .......................... 96 

6.3.  Progress with Commission recommendations ................................................................ 97 

Topic 7 Designation of Heavily Modified and Artificial Water Bodies and definition of Good 
Ecological Potential ..................................................................................................................... 99 

7.1.  Assessment of implementation and compliance with the WFD requirements in the 
second cycle for designation ..................................................................................................... 99 

7.2.  Main changes in implementation and compliance since the first cycle ........................ 101 

7.3.  Progress with Commission recommendations .............................................................. 101 

Topic 8 Environmental objectives and exemptions .................................................................... 103 

8.1.  Assessment of implementation and compliance with WFD requirements in second cycle 
 ....................................................................................................................................... 103 

8.2.  Main changes in implementation and compliance since first cycle .............................. 110 

8.3.  Progress with Commission recommendations .............................................................. 110 

Topic 9 Programme of measures ................................................................................................ 112 

9.1.  Assessment of implementation and compliance with WFD requirements in second cycle 
 ....................................................................................................................................... 112 

9.2.  Main changes in implementation and compliance since first cycle .............................. 119 

9.3.  Progress with Commission recommendations .............................................................. 119 

Topic 10 Measures related to abstractions and water scarcity .................................................. 122 

10.1.  Assessment of implementation and compliance with the WFD requirements in the 
second cycle ............................................................................................................................ 122 

10.2.  Main changes in implementation and compliance since the first cycle ..................... 123 

10.3. 

Progress with Commission recommendations ........................................................... 123 

Topic 11 Measures related to pollution from agriculture .......................................................... 124 

11.1.  Assessment of implementation and compliance with the WFD requirements in the 
second cycle ............................................................................................................................ 124 

11.2.  Main changes in implementation and compliance since the first cycle ..................... 127 

11.3. 

Progress with Commission recommendations ........................................................... 127 

Topic 12 Measures related to pollution from sectors other than agriculture ............................ 129 

12.1.  Assessment of implementation and compliance with WFD requirements in second 
cycle 

 .................................................................................................................................... 129 

12.2.  Main changes in implementation and compliance since first cycle ........................... 132 

12.3. 

Progress with Commission recommendations ........................................................... 132 

Topic 13 Measures related to hydromorphology ....................................................................... 135 

13.1.  Assessment of implementation and compliance with WFD requirements in second 
cycle 

 .................................................................................................................................... 135 

13.2.  Main changes in implementation and compliance since first cycle ........................... 136 

2 

 
 
 
13.3. 

Progress with Commission recommendations ........................................................... 137 

Topic 14 Economic analysis and water pricing policies ............................................................ 138 

14.1.  Assessment of implementation and compliance with the WFD requirements in the 
second cycle ............................................................................................................................ 138 

14.2.  Main changes in implementation and compliance since the first cycle ..................... 138 

14.3. 

Progress with Commission recommendations ........................................................... 138 

Topic 15 Considerations specific to Protected Areas (identification, monitoring, objectives and 
measures) .................................................................................................................................... 141 

15.1.  Assessment of implementation and compliance with the WFD requirements in the 
second cycle ............................................................................................................................ 141 

15.2.  Main changes in implementation and compliance since the first cycle ..................... 145 

15.3. 

Progress with Commission recommendations ........................................................... 145 

Topic 16 Adaptation to drought and climate change ................................................................. 146 

16.1.  Assessment of implementation and compliance with the WFD requirements in the 
second cycle ............................................................................................................................ 146 

16.2.  Main changes in implementation and compliance since the first cycle ..................... 146 

16.3. 

Progress with Commission recommendations ........................................................... 146 

3 

 
Acronyms and definitions 

EQS Directive 

Environmental Quality Standards Directive 

FD 

Km 

km2 

KTM 

PoM 

Floods Directive 

Kilometre 

Kilometre squared 

Key Type of Measure 

Programme of Measures 

QA/QC Directive 

Quality Assurance / Quality Control Directive  

RBD 

RBMP 

WFD 

WISE 

Annex 0 

River Basin District 

River Basin Management Plan 

Water Framework Directive 

Water Information System for Europe 

Member States reported the structured information on the 
second  RBMPs  to  WISE  (Water  Information  System  for 
Europe).  Due  to  the  late  availability  of  the  reporting 
guidance, Member States could include in the reporting an 
Annex 0, consisting of a short explanatory note identifying 
what  information  they  were  unable  to  report  and  the 
reasons  why.  This  Annex  was  produced  using  a template 
included  in  the  reporting  guidance.  If  Member  States 
reported all the required information, this explanatory note 
was not necessary. 

4 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
Foreword 

The  Water  Framework  Directive  (WFD)  (2000/60/EC)  requires  in  its  Article  18  that  each 

Member  State  reports  its  River  Basin  Management  Plan(s)  (RBMPs)  to  the  European 
Commission. The second RBMPs were due to be adopted by the Member States in December 

2015 and reported to the European Commission in March 2016. 

This  Member  State  Assessment  report  was  drafted  on  the  basis  of  information  that  was 

reported  by  Member  States  through  the  Water  Information  System  for  Europe  (WISE) 
electronic reporting.  

The  Member  State  Reports  reflect  the  situation  as  reported  by  each  Member  State  to  the 
European Commission in 2016 or 2017 and with reference to River Basin Management Plans 

(RBMP) prepared earlier. The situation in the Member States may have changed since then. 

5 

 
 
 
 
General Information 

Map A  

 Map of River Basin Districts 

Source: WISE, Eurostat (country borders) 

  International River Basin Districts (within European Union) 
  International River Basin Districts (outside European Union) 
  National River Basin Districts (within European Union) 
  Countries (outside European Union) 
  Coastal Waters 

The  information  on  areas  of  the  national  RBDs  including  sharing  countries  is  provided  in 
Table A: 

Table A: Overview of Estonia‘s River Basin Districts  

RBD 

Name 

Size (km2)  Coastal water area (km2)  Countries sharing RBD 

EE1  West-Estonian 

EE2 

East-Estonian 

23478 

19047 

12949 

1552 

EE3  Koiva 

1309 
Source: WISE electronic reporting 

0 

- 

LV, RU 

LV 

6 

EEFIVHA2FIVHA3LVGUBALVDUBALVVUBARUEE2EE1EE1EE3EE1050100kmGulf of FinlandBalticSeaGulfofRiga 
 
 
 
 
 
 
 
 
 
 
 
 
The share of Estonia in the respective international RBDs is 9.3 % (Gauja/Koiva) and 30.2 % 

(East-Estonia/Narva).  

Table B: Transboundary river basins by category and % share in Estonia 

Name international 
river basin 

National 
RBD 

Countries 
sharing 
RBD 

Gauja/Koiva 

EE3 

LV, RU 

Co-ordination category 

2 

Total 1-4 

km² 

1309 

% 

9.3 

km² 

1309 

% 

9.3 

East-Estonia/Narva 
(including Lake 
Peipsi/ChudskoeChu
dskoe, Lake 
Pihkva/Pskovskoye) 

EE2 

LV, (RU) 

17000 

30.2 

17000 

30.2 

Source: WISE electronic reporting. Estonia subsequently noted that RU shares RBD EE2. 

Category 1: International agreement, permanent co-operation body and international 
RBMP in place.  
Category 2: International agreement and permanent co-operation body in place. 
Category 3: International agreement in place. 
Category 4: No co-operation formalised. 

7 

 
 
 
Status of second river basin management plan reporting 

All three RBMPs of Estonia (National West-Estonian River Basin Management Plan, National 

East-Estonian River Basin Management Plan, National Koiva River Basin Management Plan) 
were published on 7 January 2016. Documents are available from the European Environment 

Agency (EEA) EIONET Central Data Repository https://cdr.eionet.europa.eu/.  

8 

 
 
 
Key strengths, improvements and weaknesses of the second River 
Basin Management Plans 

The main strengths and shortcomings of the second RBMPs of Estonia are as follows: 

 

Governance and public consultation 

 

A  broad  range  of  stakeholder  groups  were  actively  involved  in  the  preparation  of 

Estonia’s RBMPs, including via advisory groups. 

 

Estonia has  strengthened cooperation with  Latvia, including via the preparation of a 

common “roof report” for one RBMP.  

 

Characterisation of the RBD 

 

Improvements  to  the  delineation  of  groundwater  bodies  have  been  made,  based  on 

better knowledge and conceptual understanding of groundwater, mapping of pressures 
and the consideration of water horizons.  

 

 

 

No transitional water body has been delineated and no reason for this was provided in 
the RBMPs. 

Several  of  the  national  types  for  Estonia  in  all  of  the  RBDs  do  not  appear  to  have 
corresponding  intercalibration  types:  three  coastal  water  body,  five  lake  water  body 

and  two  river  water  body  types.  Type-specific  reference  conditions  have  only  been 
established  for  some  relevant  biological  quality  elements  and  none  were  established 

for  hydromorphological  quality  elements.  This  leads  to  some  weaknesses  in  the 
classification of status/potential according to these quality elements. 

Generally, the assessment of pressures on surface waters for the second RBMPs uses 
more  quantitative  data  and  is  more  specific  to  water  bodies.  However,  a  relatively 
high proportion of pressures are still identified as “unknown”. 

 

Inventories of emissions have been established for all RBDs for 35 of the 41 Priority 

Substances. Tier 1 of the methodology was used for several substances, including for 

some  of  the  substances  relevant  at  RBD  level,  which  is  not  in  line  with  the 
recommendation  from  the  CIS  Guidance  Document  n°28.  Tiers  1+2  was  used  for 

other substances. The data quality was uncertain or very uncertain. 

9 

 
 
  Monitoring, assessment and classification of ecological status  

 

There were significant increases in the number of surveillance monitoring sites in all 

three relevant water categories since the first RBMPs. Operational monitoring sites in 
coastal  waters  were  reported  for  the  first  time  in  the  second  RBMPs.  However,  the 

number of operational monitoring sites in lakes and rivers decreased. 

 

There are still significant gaps in the quality elements (QE) monitored for surveillance 

purposes e.g. morphological conditions and biological quality elements in some water 
categories and RBDs. 

 

For  River  Basin  Specific  Pollutants,  more  than  85  %  of  all  water  bodies  were  not 

monitored and more than 90 % were not classified. 

 

The  selection  of  River  Basin  Specific  Pollutants  seems  to  rely  on  expert  judgment. 

The  Environmental  Quality  Standards  were  set  in  accordance  with  Technical 
Guidance Document n. 27. 

 

The confidence in  classification is reported as low for most of the water bodies that 
were classified in good ecological status/potential. 

 

The number of assessment methods for biological quality element increased since the 

first RBMP for all relevant water categories. 

 

The number of water bodies in less than good ecological status/potential increased for 

all water categories in all RBDs, except lakes in the East-Estonian RBD. 

  Monitoring, assessment and classification of chemical status in surface water bodies 

 

Between  the  two  RBMPs,  there  was  a  large  decrease  in  the  proportion  of  surface 

water bodies with good chemical status from 99 % to 10 % and a significant increase 
in the proportion with unknown status from 0 to 88 %. This results from changes in 

the  assessment  methodology  and  from  the  increase  in  the  number  of  priority 
substances  monitored.  These  changes  led  to  a  more  robust  assessment  of  chemical 

status compared to the first RBMP, although in a limited proportion of water bodies. 

 

All  territorial  waters  and  almost  all  coastal  water  bodies  were  monitored  but  only 

about 20 % of inland water bodies were monitored. The status of the non-monitored 
was unknown. 

10 

 
 

All  water  bodies  classified  were  associated  with  medium  confidence  in  the 

classification. 

 

In two of the three RBDs, 39 of the 41 Priority Substances were monitored in water. 

Monitoring was performed for only four substances in the Koiva RBD. All substances 
identified  as  discharged  were  monitored  (however  not  all  Priority  Substances  are 

included  in  the  inventories,  so  it  is  unclear  whether  all  discharged  substances  were 
identified). The frequency of monitoring was lower than the recommended minimum 

frequencies for a large majority of substances.  

  Mercury,  hexachlorobenzene  and  hexabutadiene  were  monitored  in  biota  for  status 
assessment but only in what seems to be a very limited number of sites in coastal and 

territorial  waters,  in  two  of  the  three  RBDs.  The  frequency  of  monitoring  met  the 
recommended  minimum  frequency  in  a  majority  of  monitoring  sites.  No  biota 

monitoring was performed in the Koiva RBD. 

 

Trend  monitoring  in  sediment  and/or  biota  covered  several  11  of  the  14  required 

Priority  Substances  in  two  of  the  three  RBDs,  and  the  number  of  water  bodies 
monitored  appears  to  be  very  limited.  The  monitoring  was  performed  at  the 

recommended minimum frequency at some but not all sites. No trend monitoring was 
reported in the Koiva RBD. 

  Monitoring,  assessment  and  classification  of  chemical  and  quantitative  status  of 

groundwater bodies 

 

There are 39 groundwater bodies in Estonia with no monitoring for quantitative status. 

According  to  information  subsequently  provided  by  Estonia,  there  is  quantitative 
groundwater  monitoring,  which  was  not  reported,  but  not  yet  covering  all 

groundwater bodies. 

 

Groundwater dependent  ecosystems and groundwater associated surface waters have 

now been considered in the assessment. 

 

Not all groundwater bodies at risk are covered by operational monitoring and not all 

substances causing risk are covered. 

11 

 
 
 

Designation of Heavily Modified and Artificial Water Bodies and definition of Good 

Ecological Potential 

 

The methodology for heavily modified water bodies designation includes criteria for 
assessing  substantial  changes  in  character,  general  criteria  for  the  assessment  of 

significant  adverse  effects  and  provides  general  information  on  the  assessment  of 
better  environmental  options  (“other  means”).  However,  information  has  not  been 

found on the outcomes of the assessment of significant adverse effects  and of better 
environmental options for all individual heavily modified water bodies. 

 

For  the  second  RBMPs,  a  method  for  defining  good  ecological  potential  has  been 
terms  of 
developed  at  national 

level.  This  has  been  defined  mostly 

in 

hydromorphology  with  biology  being  used  to  a  limited  extent.  In  the  first  RBMPs 
good ecological potential was not defined. 

 

Environmental objectives and exemptions 

 

Environmental objectives for ecological  and  chemical  status  of surface  water bodies 

have  been  reported  in  all  RBDs  as  well  as  for  chemical  and  quantitative  status  of 
groundwater. Information is also provided on when the objectives will be achieved. 

  WFD exemptions have not been applied and justified for groundwater chemical status 

although not all groundwater bodies are in good status in 2015. 

 

There  is  still  a  lack  of  clear  criteria  for  the  application  of  "technical  feasibility", 
"disproportionate costs" and "natural conditions". 

 

Programme of Measures 

  With regard to the PoM, significant progress has been made, particularly in reducing 
uncertainties,  reporting  costs of measures,  and in identifying the  gap to  good status. 

Cost-Effectiveness analysis has been introduced to aid in the selection of measures. 

 

For  surface  waters,  KTMs  were  reported  as  operational  for  all  significant  pressures 

causing  failure  of  objectives,  and  for  most  significant  pressures  in  groundwater. 

Specific measures were reported to be operational under each of these KTMs. KTMs 
to address River Basin Specific Pollutants causing a risk of failure in surface water are 

needed in the East-Estonian RBD and Koiva RBDs. 

12 

 
  Measures related to abstractions and water scarcity 

  Water  abstraction  pressures  are  not  reported  as  relevant  for  Estonia,  with  only  one 
RBD (East-Estonian) having 5 % of groundwater bodies in bad quantitative status. 

 

The  Water  Exploitation  Index+  is  not  calculated,  but  water  quantity  data  have  been 

reported. 

  Measures related to pollution from agriculture 

 

There is a clear link between agricultural pressures and agricultural measures. At the 

time  of  PoM  drafting  a  specific  so-called  second  phase  of  the  pressure  analysis  and 

risk assessment had been carried out. During this additional pressure analysis, mapped 
pressure  sources  were  associated  with  the  status  of  the  water  body  and  the  quality 

elements causing the less-than-good status. 

 

Agricultural  measures  are  mostly  mandatory  and  their  level  of  ambition  appears 

limited. 

 

General binding rules in line with  Article 11(3)(h) WFD to  control diffuse pollution 

are applied in all basins. 

  Mandatory  safeguard  zones  are  established  around  protection  areas  that  are  used  or 

intended to be used for drinking water. 

 

Financing of measures is secured in all basins. 

  Measures related to pollution from sectors other than agriculture 

 

In the context of this topic, Estonia reported only generic measures in relation to the 

Priority Substances and other pollutants causing failure, and most of them were of an 
information-gathering nature. 

  Many  of  the  surface  water  bodies  suffering  pressures  from  urban  wastewater 
discharges  are  predicted  to  achieve  good  status  only  by  2027,  mostly  as  a  result  of 
phosphorus.  The  level  of  compliance  and  timing  to  reach  compliance  are  not 
addressed  in  detail  within  the  RBMPs,  although  a  separate  action  plan  is  said  to 

outline  the  cost  of  measures  and  the  deadlines  as  regards  improvements  to  urban 
waste water treatment. 

13 

 
  Measures related to hydromorphology 

 

Several  hydromorphological  measures  are  clearly  reported  to  address  significant 

hydromorphological  pressures  in  the  second  cycle,  while  in  the  first  RBMPs,  no 
hydromorphological measures at all had been identified by the time of adoption of the 

RBMPs.  

 

Ecological flows have been derived for all relevant water bodies in all RBDs but they 

have been partially implemented, with relevant work still ongoing. 

 

Economic analysis and water pricing policies  

 

 

In relation to Article 9, environmental and resource costs are not fully covered. 

Considerations specific to Protected Areas (identification, monitoring, objectives and 

measures) 

 

Additional individual objectives for protected Birds and Habitat Areas have not been 

set. 

 

Adaptation to drought and climate change 

 

Climate  change  was  considered  in  all  RBDs,  on  the  basis  of  the  Common 

Implementation Strategy guidance document on how to adapt to  climate change. No 

Drought Management Plans were developed.  

14 

 
 
 
Recommendations  

 

 

 

Estonia  should 

include  clear 

information 

in  national  RBMPs  on 

international 

coordination efforts in order to increase transparency.  

Estonia  should  continue  to  improve  international  cooperation,  including  coordinated 
assessments of the technical aspects of the WFD such as ensuring a harmonized approach 

for status assessment and a coordinated PoM in order to ensure the timely achievement 
of the WFD objectives. 

Estonia  needs  to  delineate  adequately  transitional  water  bodies  or  provide  a  clear 
explanation for their non-existence. 

  Work on the identification of pressures and their apportionment among sectors needs to 
continue, as several of them are reported as unknown. This is necessary so that adequate 
measures can be put in place. 

 

 

 

Reference  conditions  need  to  be  established  for  all  relevant  Quality  Elements  for  all 
surface waters. 

Inventories  of  emissions,  discharges  and  losses  of  chemical  substances  need  to  be 
completed. 

Estonia  should  further  improve  monitoring  of  surface  water  to  ensure  meeting  WFD 

requirements,  as  there  are  still  significant  gaps  and  there  has  been  a  decrease  in  the 
number of operational monitoring sites in lakes and rivers. Monitoring should cover all 

relevant  quality  elements  in  all  water  categories  both  in  surveillance  and  operational 
monitoring.  Monitoring  frequencies  should  be  in  line  with  the  minimum recommended 
frequency, especially for surveillance monitoring, unless adequately justified. 

 

Estonia  should  have  a  clear  and  transparent  method  for  the  selection  of  River  Basin 

Specific  Pollutants  and  provide  clear  information  on  how  their  status  is  determined. 
Estonia  should  develop,  for  all  River  Basin  Specific  Pollutants,  Environmental  Quality 

Standards  that  meet  the  minimum  requirements  for  the  protection  of  freshwater  and 
marine ecosystems from possible adverse effects, as well as of human health. 

 

Estonia  should  continue  and  step  up  efforts  to  assess  the  status  of  all  water  bodies. 
Monitoring  should  be  performed  in  a  way  that  provides  sufficient  temporal  resolution 

and spatial coverage (including in biota), to reach sufficient confidence in the assessment 
for  all  water  bodies,  if  necessary  in  combination  with  robust  extrapolation/grouping 

methods.  If  a  different  matrix  or  reduced  frequencies  are  used,  the  corresponding 
explanations should be provided, as required by the Directive. 

15 

 
 

Trend monitoring should be  further improved to  ensure that  all the relevant  substances 

specified  in  Directive  2008/105/EC  are  monitored  in  a  way  that  provides  sufficient 
spatial coverage and temporal resolution, in all RBDs. 

 

 

 

 

Estonia  needs  to  continue  working  towards  a  cleared  status  assessment  and  improved 
level of confidence for groundwater bodies through better operational monitoring. 

The review of the assessment of groundwater status needs to be completed. 

Efforts  need  to  be  continued  to  fully  meet  all  the  requirements  of  Article  4(3)  in  a 
transparent way. Significant adverse effects on the use or the wider environment and the 

lack of significantly better environmental options need to be defined and specified. This 
will ensure transparency in the process of designation and objective setting. 

If  water  bodies  are  failing  to  achieve  the  WFD  environmental  objectives,  exemptions 
need  to  be  justified.  Estonia  did  not  apply  WFD  exemptions  for  the  chemical  status  of 

groundwater bodies although not all groundwater bodies are in good status, but applied 
exemptions according to the Groundwater Directive. The understanding of the different 

nature  of  exemptions  according  to  the  WFD  and  Groundwater  Directive  needs  to  be 
improved and exemptions properly applied. 

 

Estonia  should  continue  to  improve  transparency  and  uncertainty  in  the  justification  of 

exemptions  by  developing  and  applying  clear  criteria  for  technical  feasibility, 
disproportionate  costs  and  natural  conditions  for  the  application  of  Article  4(4).  These 
need to be clearly distinguishable from the criteria and justifications for the application 

of Article 4(5) exemptions. 

 

A thorough assessment of proposed new modifications should be ensured in line with the 

requirements of the WFD and as further specified by the Judgment of the Court in case 

C-461/13.  The  RMBPs  should  clarify  whether  impacts  of  proposed  new  projects  were 
assessed.  In  case  of  expected  deterioration  or  non-achievement  of  good  status/potential 

ensure that the project can only be authorised in case the specific conditions as outlined 
in  WFD  Article  4(7)  are  fulfilled.  All  conditions  for  the  application  of  Article  4(7)  for 

individual projects must be included and justified in the RBMPs as early  in the project 
phase as possible which will allow for improved transparency. 

 

In the third RBMPs, Estonia should clearly state to what extent, in terms of area covered 
and  pollution  risk  mitigated,  basic  measures  (minimum  requirements  to  be  complied 

with)  or  supplementary  measures  (designed  to  be  implemented  in  addition  to  basic 
measures)  will  contribute  to  achieving  the  WFD  objectives  and  identify  sources  of 

funding (e.g. CAP Pillar 1, RDP), as appropriate, to facilitate successful implementation 

16 

 
of  these  measures.  Explicit  links  in  the  RBMPs  between  the  WFD  and  supporting 

programmes and instruments (e.g. ND, RDP etc.) need to be ensured and both nitrogen 
and phosphorus shall be included in the general binding rules. 

 

 

 

Estonia should take a more ambitious approach to tackling non-agricultural pollution by 
identifying  substance-specific  measures  that  go  beyond  information-gathering  actions, 

and  by  assessing  the  effectiveness  of  planned  measures  and  applying  supplementary 
measures where necessary to achieve the objectives. 

Estonia  should  continue  its  efforts  to  establish  ecological  flows  for  all  relevant  water 
bodies, and ensure its implementation as soon as possible. 

Estonia should continue prioritising the use of green infrastructure and/or natural water 

retention  measures  that  provide  a  range  of  environmental  (improvements  in  water 
quality, flood protection, habitat conservation etc.), social and economic benefits which 

can be in many cases more cost-effective than grey infrastructure. 

 

Cost  recovery should be applied for water use activities having a significant  impact  on 

water bodies. Any exemption should be justified using Article 9(4). Estonia should also 
present  in  a  transparent  manner  how  financial,  environmental  and  resource  costs  have 

been calculated and how the adequate contribution of the different users is ensured. The 
water-pricing  policy  should  be  set  out  in  a  transparent  fashion  and  a  clear  overview  of 

estimated investments and investment needs should be provided. 

 

There seems to be little or no progress on the assessment on the water requirements of 

Birds and Habitat Directives Protected Areas in order to achieve favourable conservation 
status. Further work is needed to address this issue. 

17 

 
 
 
Topic 1

 Governance and public participation 

1.1

Assessment  of 
requirements in second cycle 

implementation  and  compliance  with  WFD 

1.1.1  Administrative arrangements – river basin districts 

Estonia  prepared  three  River  Basin  Management  Plans  (RBMPs),  one  for  each  of  its  River 
Basin Districts (RBDs): West-Estonian, East-Estonian and Koiva.  

Two of Estonia's RBDs are part of international RBDs: East-Estonian is part of an international 

RBD shared with Latvia and Russia (including Lakes Peipsi/Chudkoe and Pihkva/Pskovskoye, 
shared with Russia); Koiva is part of an international RBD shared with Latvia. 

1.1.2  Administrative arrangements – competent authorities 

Estonia reports three competent authorities: The Ministry of Environment, the Environmental 

Board  and  the  Environment  Agency.  The  Ministry  of  Environment’s  main  roles  are: 
enforcement  of  regulations;  economic  analysis;  preparation  of  the  RBMP  and  PoM;  public 

participation,  and;  coordination  of 
the  Estonian 
Environmental Board is the implementation of measures. The Estonian Environment Agency is 

implementation.  The  main  role  of 

responsible for the monitoring and assessment of groundwater and surface water, pressure and 
impact analysis and reporting to the Commission.  

This  represents  a  change  from  the  previous  cycle:  the  2012  Commission  Staff  Working 

Document  for  the  first  cycle  reports  the  Ministry  of  the  Environment  as  the  competent 
authority for all of Estonia's RBDs. 

1.1.3  River  Basin  Management  Plans  –  structure  and  Strategic  Environmental 

Assessments 

Estonia does not have sub-plans for its RBMPs. 

Estonia  did  not  report  that  Strategic  Environmental  Assessments  had  been  carried  out  for  its 
RBMPs. 

18 

 
 
 
1.1.4 

Public consultation 

For  all  three  RBMPs,  the  public  and  interested  parties  were  informed  by:  direct  mailing, 
Internet,  invitations  to  stakeholders,  local  authorities,  media  (papers,  TV,  radio),  meetings, 

printed  material  and  social  networking.  Documents  were  available  for  download  and  paper 
copies  were  available  in  municipal  buildings.  Documents  were  available  for  the  requisite  6 

months. There was no international coordination of public participation. 

For all three RBDs, the following stakeholders were actively involved in the development of 

the  RBMPs:  agriculture/farmers,  energy/hydropower,  fisheries/aquaculture,  local/regional 
authorities, NGOs/nature protection and water supply and sanitation.  

The  mechanisms  for  active  involvement  were:  the  establishment  of  advisory  groups, 

involvement in drafting and regular exhibitions. 

For  all  three  RBDs,  public  consultation  had  the  following  impacts:  addition  of  new 
information,  adjustment  to  specific  measures,  changes  to  the  selection  of  measures, 

commitment to action in the next RBMP cycle and commitment to further research. 

1.1.5 

Integration  with  the  Floods  Directive  and  the  Marine  Strategy  Framework 

Directive 

A joint consultation process was carried out for the RBMPs and Flood Risk Management Plans 
prepared under the Floods Directive1. 

For  West-Estonian  and  East-Estonian,  joint  consultation  was  held  with  the  Marine  Strategy 
Framework Directive2. 

1.1.6 

International coordination and cooperation 

As noted above, East-Estonian is part of an international RBD shared with Latvia and Russia 

and Koiva is part of international RBD shared with Latvia. For both, Estonia reports that there 
is  an  international  agreement  and  a  permanent  co-operation  body  in  place  (designated  as 

category 2). 

1  Estonia  reported  to  WISE  that  the  RBMPs  and  FRMPs  were  integrated  into  joint  plans.  This  was  a  reporting 
error.  RBMPs and Flood Risk Management Plans are separate plans.  
2 Directive 2008/56/EC of the European Parliament and of the Council of 17 June 2008 establishing a framework 
for  community  action  in  the  field  of  marine  environmental  policy  (Marine  Strategy  Framework  Directive) 
http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32008L0056 

19 

 
                                                      
The  RBMP  for  Koiva  states  that  international  co-operation  with  Latvia  is  based  on  an 

agreement between the Estonian and Latvian Ministries of Environment. Areas of cooperation 
included: characterisation, joint monitoring, pressures/measures assessment, economic analysis 

and water pricing, and a joint communication strategy and public participation activities. The 
RBMP for East-Estonian, part of an RBD shared with both Latvia and Russia, does not discuss 

transboundary cooperation with Latvia. 

A “roof  report” has been prepared for the RBDs shared with  Estonia, as  Latvia informed: in 

2016,  Latvian  and  Estonian  experts  together  produced  a  background  document  for  the 
Koiva/Gauja  RBD,  which  among  the  other  things  includes  measures  proposed  in  both 

countries. The background document was approved by Estonian and Latvian water directors. 

Estonia’s  co-operation  with  Russia  occurs  within  the  framework  of  the  Joint  Committee  for 
Estonian-Russian Transboundary Water Bodies, created in 1997, including two expert groups 

under  the  Joint  Committee,  one  for  monitoring  and  assessment  and  the  other  for  integrated 
water  management.  Estonia  subsequently  clarified  that  co-operation  in  the  frame  of  the  first 

expert  group  includes  environmental  monitoring  and  assessment  of  transboundary  water 
bodies, while the second group’s task is related to issues on transboundary water management 

and  implementation  of  related  measures  under  RBMPs.  The  expert  groups  and  the  Joint 
Committee meet at least once per year; their work includes analysis of the implementation of 

RBMPs.  

1.2

  Main changes in implementation and compliance since first cycle 

The 2012 Commission Staff Working Document for the first cycle reports the Ministry of the 
Environment as the sole competent authority for all Estonia's RBDs. In the WISE reporting for 

the  second  cycle,  three  bodies  are  identified:  the  Ministry  of  Environment,  the  Estonian 
Environment Agency (created in 2013) and the Estonian Environment Board. 

1.3

Progress with Commission recommendations 

  Recommendation: Ensure coherent trans-boundary cooperation in PoMs development 

(with Latvia).  

Assessment: The international coordination category for both East-Estonian and Koiva, 
both  shared  with  Latvia,  in  the  second  cycle  is  the  same  as  that  in  the  first  cycle: 

category  2  (i.e.  international  agreement  and  permanent  cooperation  body  in  place). 

20 

 
 
Consequently, international Programmes of Measures have not been prepared for these 

RBDs. 

The RBMP for Koiva states that international co-operation with Latvia is based on an 

agreement  between  the  Estonian  and  Latvian  Ministries  of  Environment.  Areas  of 
joint  monitoring,  pressures/measures 
cooperation 

characterisation, 

included: 

assessment,  economic  analysis/water  pricing  and  a  joint  communication  strategy  and 
public  participation  activities.  The  RBMP  for  East-Estonian,  part  of  an  RBD  shared 

with both Latvia and Russia, does not discuss transboundary cooperation with Latvia.  

In  2016,  however,  Estonian  and  Latvian  officials  prepared  a  “roof  report”  for  the 
Koiva/Gauja  RBD,  which  among  other  topics  discussed  measures  in  the  national 

RBMPs.   

Consequently, Estonia has partially implemented the recommendation. 

21 

 
 
 
Topic 2 Characterisation of the River Basin District 

2.1.  Assessment  of 

implementation  and  compliance  with  the  WFD 

requirements in the second cycle  

2.1.1. Delineation of water bodies and designation of heavily modified and artificial water 

bodies 

Overall, the number of surface water bodies remained largely the same between the first and 

second RBMPs (Table 2.1). New territorial water bodies were delineated in the West-Estonian 
and  East-Estonian  RBDs  for  the  second  RBMP.  In  the  second  RBMP,  74  %  of  identified 

surface  water  bodies  were  natural,  20  %  were  designated  as  heavily  modified  and  6  %  as 
artificial water bodies. The situation was fairly similar in the first RBMPs, as shown in Figure 

2.1.  The  water  uses  and  physical  alterations  have  been  reported  for  each  heavily  modified 
water body category. 

For groundwater bodies, there was a 50 % increase in total number from the first to the second 
RBMPs, with this increase seen across all RBDs (Table 2.3). Across all three RBDs a total of 

13 groundwater bodies were added to the 26 groundwater bodies initially delineated in the first 
RBMPs. It is explained that the objective of establishing a larger number of smaller bodies of 

groundwater  was  to  better  organise  the  protection  of  their  chemical  and  quantitative  status. 
Based on the information found in the RBMPs, groundwater bodies that were not previously 

delineated  according  to  the  boundaries  of  the  RBD  are  now  delineated  clearly  within  the 
RBDs. In terms of groundwater pressure sources, they have been more thoroughly mapped and 

identified  in  the  second  cycle,  making  it  possible  to  better  delineate  groundwater  bodies.  In 
addition, new groundwater bodies were delineated in areas where more than 10 m3 per day was 
abstracted from the aquifer but where a groundwater body had not previously been delineated.  

The delineation of the groundwater bodies and description of boundaries and hydrogeological 
conceptual  models  has  been  compiled  in  accordance  with  the  Common  Implementation 

Strategy  Guidance  n.  26,  "Risk  Assessment  and  the  Use  of  Conceptual  Models  for 
Groundwater"  (2011)3.  Better  knowledge  and  conceptual  understanding  of  groundwater  was 
achieved in the second RBMPs thanks to the work done in 2012 "Description of the boundaries 
of  groundwater  bodies  and  the  development  of  hydrogeological  conceptual  models  of 

groundwater  bodies",  as  explained  in  the  RBMPs.  In  particular,  Estonia  has  considered  the 

3  European  Commission  (2011)  Guidance  on  Risk  Assessment  and  the  Use  of  Conceptual  Models  for 
Groundwater. ISBN-10: 3845458917. 

22 

 
                                                      
hydrostratigraphic position of the water layers, the location in terms of the RBDs, the coastline 

and the state border.  

Table 2.1 

Number and area/length of delineated surface water bodies in Estonia for the 

second and first cycles 

Year  RBD 

2016  EE1 

2016  EE2 

2016  EE3 

 2016  Total 

2010  EE1 

2010  EE2 

2010  EE3 

2010  Total 

Lakes 

Rivers 

Coastal waters 

Number 
of water 
bodies 

Total 
area 
(km2) of 
water 
bodies 

Number 
of water 
bodies 

41 

41 

7 

89 

41 

40 

8 

89 

71 

1,898 

8 

1,978 

71 

1,885 

9 

1,966 

358 

268 

19 

645 

358 

267 

20 

645 

Total 
length 
of water 
body 
(km) 

6,078 

5,152 

364 

11,594 

6,320 

5,413 

374 

Number 
of water 
bodies 

Total 
area 
(km2) of 
water 
bodies 

14 

12,965 

2 

0 

16 

14 

2 

0 

1,553 

0 

14,518 

12,949 

1,552 

0 

12,106 

16 

14,501 

Source: WISE electronic reporting  

Figure 2.1 

Proportion of surface water bodies in Estonia designated as artificial, heavily 
modified  and  natural  for  the  second  and  first  cycles.  NB  -  the  numbers  in 

parenthesis are the numbers of water bodies in each water category. 

100%
90%
80%
70%
60%
50%
40%
30%
20%
10%
0%

Artificial
97% 

97% 

Heavily Modified

Natural

94% 

94% 

71% 

70% 

23% 

24% 

7% 

7% 

Rivers
2016
(645)

Rivers
2010
(645)

6% 

0% 

6% 

0% 

Coastal
2016 (16)

Coastal
2010 (16)

3% 

0% 

3% 

0% 

Lakes
2016 (89)

Lakes
2010 (89)

Source: WISE electronic reporting 

Table 2.2 shows the differences in size distribution of surface water bodies between the second 

and first cycles. The size distribution largely remained the same between the two cycles. The 

23 

 
 
 
 
minimum size criteria reported were 10 km2 catchment area for rivers and 0.5 km2 surface area 
for lakes.  

Table 2.2 

Size  distribution  of  surface  water  bodies  in  Estonia  in  the  second  and  first 

cycles 

Lake area (km2) 

River length (km) 

Coastal (km2) 

Year 

RB
D 

Min  Max 

Averag
e 

Min  Max 

Averag
e 

Min 

Max 

2016 

EE1 

0.2 

9.41 

1.74 

2.62 

4.16 

3.39 

2016 

EE2 

0.02 

1,511.
55 

2016 

EE3 

0.12 

2.33 

46.3 

1.16 

0.7 

18.2
1 

6.61 

42.3 

596.0
8 

Averag
e 

926.07 

5,549.
09 

956.77 

776.42 

2010 

EE1 

0.2 

9.41 

1.74 

2.63 

4.16 

3.4 

42.18 

2010 

EE2 

0.02 

1,495.
69 

47.13 

0.58 

17.8
9 

5.02 

596.1
9 

5,543.
93 

924.95 

956.04 

776.12 

2010 

EE3 

0.11 

2.33 

1.15 

Source: WISE electronic reporting 

Table 2.3 

Number and area of delineated groundwater bodies in Estonia for the second 
and first cycles 

Year 

RBD 

Number 

2016 

2016 

2016 

2016 

2010 

2010 

2010 

2010 

EE1 

EE2 

EE3 

Total 

EE1 

EE2 

EE3 

Total 

16 

20 

3 

39 

10 

14 

2 

26 

Area (km2) 

Minimum 

Maximum 

Average 

1.4 

8.9 

20,501.46 

3,653.55 

11,811.44 

2,617.75 

172.31 

1,309.03 

738.8 

117 

25 

446 

20,547.00 

6,088.20 

13,024.00 

4,160.93 

1,334.00 

890 

Source: WISE electronic reporting.  

Table 2.4 summarises the information reported by Estonia on how water bodies have evolved 

between the two cycles. It shows that the main changes were for groundwater bodies with the 
aggregation of water bodies and the creation of new ones. 

24 

 
 
 
 
 
 
 
 
 
  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Table 2.4 

Type  of  change  in  delineation  of  groundwater  and  surface  water  bodies  in 

Estonia between the second and first cycles 

Type of water body change for second 
cycle  

Groundwater 
Body 

Lake Water 
Body 

River 
Water Body 

Coastal 
Water Body 

Aggregation 

Splitting 

Aggregation and splitting 

Change in code 

Extended area 

Creation 

Deletion 

No change 

Total water bodies before deletion 

Delineated for second cycle (after deletion 
from first cycle) 

12 

8 

13 

4 

2 

26 

65 

39 

89 

89 

645 

645 

16 

16 

2.1.2. Identification of transboundary water bodies  

Source: WISE electronic reporting  

Transboundary  river  water  bodies  have  been  designated  for  each  RBD,  transboundary  lake 
water bodies in East-Estonian and Koiva and one transboundary coastal water body in West-

Estonian. No transboundary groundwater bodies have been identified.  

The delineation of transboundary surface water bodies with neighbouring Latvia (Koiva RBD) 

was one of the objectives of a project  (Gauja/Koiva project  in  the  years  2011-2013) that has 
been  mentioned  in  the  RBMP.  There  is  no  explicit  information  in  the  East-Estonian  RBMP 

about the delineation of transboundary water bodies with Russia. 

2.1.3. Typology of surface water bodies 

The  number  of  surface  water  body  types  appears  to  have  decreased  overall  by  about  20  % 

between  the  first  and  second  RBMPs  (Table  2.5).  Member  States  were  asked  to  report  ‘Not 
applicable’ if there is no corresponding intercalibration type for national types. Many national 

types  (heavily  modified,  artificial  and  natural)  have  been  intercalibrated.  Several  of  the 
national  types  for  Estonia  in  all  of  the  RBDs  do  not  appear  to  have  corresponding 

intercalibration types: three coastal water body, five lake water body and two river water body 
types. 

For  the  Koiva  RBD  (shared  with  Latvia)  typologies  were  adjusted  for  transboundary  surface 
water bodies under the 2011-2013 project. One of the recommendations of the project was to 

adjust the typology and the classification of the quality between the two countries. This is on-

25 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  
 
  
  
 
 
 
 
going  work  that  will  continue  in  the  third  cycle.  For  the  East-Estonian  RBD  (shared  with 

Russia) there is no evidence that the typology has been coordinated with Russia.  

Table 2.5 

Number of surface water body types at RBD level in Estonia for the first and 
second cycles 

RBD 

EE1 

EE2 

EE3 

TOTAL 

Rivers 

Lakes 

Coastal 

2010 

2016 

2010 

2016 

2010 

2016 

9 

9 

12 

5 

6 

5 

7 

3 

3 

4 

5 

7 

3 

8 

3 

0 

3 

5 

1 

0 

6 

Source: WISE electronic reporting  
Note that the total is not the sum of the types in each RBD as some types are shared by RBDs. 

2.1.4. Establishment of reference conditions for surface water bodies 

Table  2.6  shows  the  percentage  of  surface  water  body  types  in  Estonia  with  reference 

conditions.  Type-specific reference conditions  have been established  for some or all relevant 
biological quality elements and all physicochemical quality elements. Type-specific reference 

conditions do not appear to have been established for hydromorphological quality elements in 
rivers but have been established for 50 % of types in lakes. 

In  the  second  RBMPs  there  is  no  information  about  the  coordination  of  the  identification  of 
type-specific reference conditions with neighbouring countries. It is stated in the RBMPs that 

coordination of the  approaches  and methods of the main aspects  of water management  plans 
would be an objective to be addressed possibly in future projects (for the third cycle). 

Table 2.6 

Percentage  of  surface  water  body  types  in  Estonia  with  reference  conditions 
established for all, some and none of the biological, hydromorphological and 

Water 
category 

Lakes (8) 

Rivers (7) 

Coastal (6) 

physicochemical quality elements. Numbers in parenthesis are the number of 
types in each category. 

Water types 

Biological quality 
elements 

Hydromorphological 
quality elements 

Physicochemical 
quality elements 

100% 

100% 

100% 

All 

Some 

None 

All 

Some 

None 

All 

Some 

None 

100% 

100% 

100% 

50% 

50% 

100% 

100% 

Source: WISE electronic reporting  

26 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2.1.5. Characteristics of groundwater bodies  

The geological formation of the aquifer types in which groundwater bodies reside, along with 
details of whether groundwater bodies are layered or not, is reported. Further characterisation 

work has been reported since the first cycle with the inclusion of the assessment of linkages to 
surface water bodies and terrestrial ecosystems. 

2.1.6. Significant pressures and impacts on water bodies 

For surface waters, in the second RBMPs, unknown anthropogenic pressure was reported for 

71 % of water bodies. The most significant pressures on surface water bodies were reported to 
be dams, barriers and locks affecting 25 % of water bodies (Figure 2.2). In the first RBMPs, 

Estonia only reported pressures at an aggregated level making it difficult to compare reporting 
in 
of  pressures  between 

two  cycles.  There  has  been  an  apparent 

increase 

the 

hydromorphological  pressures  (Figure  2.3)  and  unknown  anthropogenic  pressures  (or  other 
pressures).  

For  groundwater  bodies,  “no  significant  pressure”  was  reported  for  77  %  of  groundwater 

bodies. The most significant pressures reported were point - contaminated sites or abandoned 
industrial sites (15 %), diffuse - contaminated sites or abandoned industrial sites (13 %), point - 

waste disposal sites (13 %) and diffuse - discharges not connected to sewerage network (13 %) 
(Figure 2.2). 

In the second RBMPs it was reported that nine pressures were not assessed for surface waters, 
including introduced species and diseases. The criteria for the identification of pressures have 

been described more specifically in a background document of the second RBMPs. The basis 
for the distribution of pressures in Estonia was an indicative list of potential pressure sources 

presented in the Guidance for reporting under the WFD.  

27 

 
 
 
Figure 2.2 

The  10  most  significant  pressures  on  surface  water  bodies  and  groundwater 
bodies in Estonia for the second cycle4 

Source: WISE electronic reporting 

4  Estonia  subsequently  clarified  that  there  were  problems  using  the  “No  significant  pressure”  option  in  the 
reporting system. Correct numbers for Estonia are: “unknown pressure” 9 % of WB (68 WB) and “No significant 
pressure” 466 WB. 

28 

 
 
 
 
 
                                                      
In the second RBMPs, the most significant impact on surface water bodies was classified as an 
“unknown  impact  type”  (67  %  of  water  bodies5),  followed  by  altered  habitats  due  to 
morphological changes (21 %). The situation was similar in groundwater bodies, with 77 % of 
water bodies with reported impacts classified as unknown6. Estonia did not report on impacts 
in the first RBMPs. 

In  the  second  RBMPs  a  relatively  high  proportion  of  pressures  are  still  classified  as 
“unknown”.  It  is  explained  that  in  these  cases  the  reason  for  the  poor  status  is  unclear  or 

unknown and the pressure sources for the water body are uncertain. The RBMPs reported that 
investigative monitoring in the catchment areas with unknown impacts is planned, which will 

help provide an overview of the water body and the pressures, after which further steps would 
be taken to improve the status of the water body to good.  

Figure 2.3  Comparison of pressures on surface water bodies in Estonia  in the first  and 

second  cycles.  Pressures  presented  at  the  aggregated  level.  NB  -  there  were 
750 identified surface water bodies for the second cycle and 754 for the first 

cycle 

Source: WISE electronic reporting 

5  Estonia  subsequently  clarified  that  there  has  been  a  reporting  error  and  58.4  %  of  water  bodies  have  “no 
significant impact”. 
6  Estonia  subsequently  clarified  that  there  has  been  a  reporting  error  and  77  %  of  water  bodies  have  “no 
significant impact”. 

29 

 
 
 
                                                      
Figure 2.4 

Significant impacts on surface water and groundwater bodies in  Estonia for 
the second cycle. Percentages of numbers of water bodies7 

Source: WISE electronic reporting  

7  Estonia  subsequently  clarified  that  there  has  been  a  reporting  error  and  surface  water  should  be  58.4  %  “no 
significant impact” and groundwater 77 % “no significant impact”. 

30 

 
 
 
 
 
                                                      
2.1.7. Definition and assessment of significant pressures on surface waters 

For surface waters, a combination of both expert judgement and numerical tools were used for 
defining pressures from point sources, diffuse, abstraction and other significant pressures. The 

significance  of  pressure  sources  was  determined  in  the  first  RBMPs  using  mostly  expert 
judgment. For the second RBMPs more quantitative data was used such as data from land and 

water use.  In the second RBMPs, the pressures assessment was more precisely presented, by 
water body, rather than generalised, identifying the pressures on the basis of the boundary of 

the catchment area and the geographic location of the pressure sources.  

Significance  of  pressures  is  reported  to  have  been  defined  in  terms  of  thresholds.  Pressures 

have  been  assessed  on  the  basis  of  the  following  categories:  point  sources,  diffuse  sources, 
water  abstraction,  water  flow  regulation  or  morphological  alterations,  use  of  surface  water 

bodies and use of coastal water.  

To  determine  pressure  sources,  including  significant  ones,  the  risk  of  not  achieving  the 
environmental objectives for water bodies due to various pressure sources was analysed, taking 

into account the trends affecting pressure sources and the likelihood of the trend development. 
The  probable  vulnerability  to  pressures  was  classified  as:  at  risk,  possibly  at  risk,  and  not  at 

risk.  The  risk  was  reported  to  be  based  on  two  aspects:  1)  whether  or  not  the  environmental 
objectives  have  been  achieved;  and  2)  identifying  the  pressures  from  human  activity  that 

caused the failure to achieve the environmental objectives.  

The mapped pressure sources were then linked to the status of the water body and to quality 

elements  displaying  poor  status.  As  a  result  of  the  analysis,  it  was  determined  whether  the 
effect of the pressure source actually influences the status of the water body. It is stated in the 

RBMPs that a clear link was established between the status and pressure sources.  

2.1.8. Definition and assessment of significant pressures on groundwater 

For groundwater it was  reported that a combination of expert judgement  and numerical tools 

were  used  to  define  diffuse  and  point  source  pressures,  abstractions  and  artificial  recharge. 
Information  about  the  tools  used  to  define  significant  pressures  on  groundwater  bodies  is 

provided in the available background document "Programme of measures and actions to reduce 
pressures  that  cause  risk  of  damage  and  poor  status  of  groundwater  bodies"  (2015).  A 

significant pressure on a groundwater body is defined as a pressure from human activity, which 
may  deteriorate  the  status  of  the  groundwater  body.  Conceptual  models  together  with 

hydrogeological models and expert judgement were used.  

31 

 
The  significance  of  pressures  is  reported  to  be  defined  in  terms  of  thresholds.  The  list  of 

polluting  substances  that  are  a  risk  to  groundwater  and  their  thresholds  were  reported  not  to 
have changed since the first RBMPs. The significance of pressures is reported not to be linked 

to the potential failure of objectives. 

2.1.9. Groundwater bodies at risk of not meeting good status 

In two of the three RBDs, 13-45 % of groundwater bodies were reported to be at risk of failing 
to meet good chemical status. The pollutants putting groundwater bodies at risk of failing good 

chemical status have been reported. 

In two of the three RBDs 19-25 % of groundwater bodies were reported to be at risk of failing 
to meet good quantitative status.  

2.1.10.  Quantification of gap to be filled and apportionment of pressures 

The  Priority  Substances  and  other  substances  causing  failure  of  good  chemical  status  have 
been reported. Measures to tackle these substances to achieve good status by 2021 have been 
reported  and  the  indicator  gap  is  reported  to  be  zero  (i.e.  good  status  to  be  reached)  for  all 

substances. 

2.1.11.  Inventories of emissions, discharges and losses of chemical substances 

Article  5  of  the  Environmental  Quality  Standards  Directive8  requires  Member  States  to 
establish  an  inventory  of  emissions,  discharges  and  losses  of  all  Priority  Substances  and  the 
eight other pollutants listed in Part A of Annex I EQS Directive for each RBD, or part thereof, 

lying  within  their  territory.  This  inventory  should  allow  Member  States  to  further  target 
measures to tackle pollution from priority substances. It should also inform the review of the 

monitoring networks, and allow the assessment of progress made in reducing (or suppressing) 
emissions,  discharges  and  losses  for  priority  substances.  Estonia  reported  that  35  of  the  41 

Priority Substances and groups of Priority Substances were included in the inventories for each 
RBD.  The  Priority  Substances  and  groups  of  priority  substances  not  included  in  any  of  the 

inventories were:  tetrachloroethylene, the group of polycyclic aromatic hydrocarbons, carbon 
tetrachloride,  trichloroethylene,  cyclodiene  pesticides  (aldrin,  dieldrin,  endrin,  isodrin),  and 

DDT  (total  DDT  and  DDT-p,p’).  The  two-step  approach  from  the  Common  Implementation 

8 Directive 2008/105/EC of the European Parliament and of the Council of 16 December 2008 on environmental 
quality  standards  in  the  field  of  water  policy,  amending  and  subsequently  repealing  Council  Directives 
82/176/EEC,  83/513/EEC,  84/156/EEC,  84/491/EEC,  86/280/EEC  and  amending  Directive  2000/60/EC  of  the 
European Parliament and of the Council  
http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32008L0105  

32 

 
                                                      
Strategy  Guidance  Document  n°289  has  been  followed  for  all  substances  considered  in  the 
inventories. Tier 1 of the methodology was implemented for most of the substances included in 
the  inventories  (including  some  substances  deemed  relevant  at  RBD  level).  For  a  limited 

number of substances a combination of Tier 1 (point source information) and Tier 2 (riverine 
load) was implemented. The data quality was assessed as uncertain or very uncertain. 

The reasons for the inventory not being complete for all Priority Substances and pollutants are 
presented in the Annex 2 of the RBMPs. It was reported that the information on substances not 

included was insufficient during the reference period (2008-2010). The following reasons were 
listed: 1) no information on the quantities of substances, both in terms of imports and usage; 2) 

no information on the content of hazardous substances in products; 3) insufficient monitoring 
data  (due  to  the  high  cost  of  analyses  and  results  below  the  limit  of  detection);  4)  unclear 

effects  on  the  aquatic  biota;  5)  information  obtained  about  hazardous  substances  from  the 
environmental permits during the reference period was limited. 

2.2.  Main changes in implementation and compliance since the first cycle 

Overall  the  number  of  surface  water  bodies  remained  the  same  between  the  first  and  second 
RBMPs. For groundwater bodies there was a 50 % increase in total number between the first 

and second RBMPs. In the second cycle, 74 % of identified surface water bodies were natural 
with  20  %  being  designated  as  heavily  modified  and  6  %  as  artificial  water  bodies.  This  is 

similar to the first cycle. The number of surface water body types appears to have decreased 
overall by about 20 % between the first and second RBMPs.  

In the first RBMPs, Estonia only reported pressures at an aggregated level and therefore it is 
difficult to compare reporting of pressures between the two cycles. Since the first RBMPs there 

has  been  an  apparent  increase  in  hydromorphological  pressures  and  unknown  anthropogenic 
pressures (or other pressures) for surface water bodies.  

2.3.  Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first PoM requested action 

on the following: 

9CIS 
Inventoryhttp://ec.europa.eu/environment/water/water-framework/facts_figures/guidance_docs_en.htm 

Preparation 

Substances 

Guidance 

Priority 

N° 

28 

of 

- 

Emissions 

33 

 
 
 
                                                      
 

Recommendation:  Where 

there  are  currently  high  uncertainties 

in 

the 

characterisation  of  the  RBDs,  identification  of  pressures,  and  in  the  assessment  of 
status,  these  need  to  be  addressed  in  the  current  cycle,  to  ensure  that  adequate 

measures can be put in place before the next cycle. 

 

Recommendation: Focus in the second RBMP on better linking pressures to impacts 

and measures, including by source apportionment, and provide a clear assessment of 
how many of the pressures (and their sources) have to be reduced to achieve the WFD 

goals. 

 

Recommendation: Describe clearly in the second RBMPs how status will be derived 

for  non-  monitored  water  bodies  and  to  restrict  and  streamline  the  use  of  expert 

judgement. 

Assessment: In the first RBMPs, Estonia only reported pressures at an aggregated level, which 

makes  it  difficult  to  compare  reporting  of  pressures  between  the  first  and  second  RBMPs. 
There  has  been  an  apparent  increase  in  hydromorphological  pressures  and  unknown 

anthropogenic pressures (or other pressures).  

In  the  second  RBMPs  a  relatively  high  proportion  of  pressures  are  still  classified  as 

“unknown”.  It  is  explained  that  in  these  cases  the  reason  for  the  poor  status  is  unclear  or 
unknown and the pressure sources for the water body are uncertain. The RBMPs reported that 

investigative monitoring in the catchment areas with unknown impacts is planned, which will 
help provide an overview of the water body and the pressures, after which further steps would 

be taken to  improve the  status  of the water body to  good.   The relatively high proportion of 
pressures that were classed as “unknown”  and the fact that further monitoring data is reported 

to  be  required,  indicates  that  further  improvement  should  be  made  in  defining  pressures  and 
impacts and linking them together. 

For both surface waters and groundwater bodies, the significance of pressures is reported to be 

defined  in  terms  of  thresholds  but  not  to  be  linked  to  the  potential  failure  of  objectives. 
However, the RBMPs show that there is a link to status in the assessment of significance for 

both surface water and groundwater. The RBMPs also show that the methods for determining 
significance  for  the  second  RBMPs  are  based  on  more  quantitative  tools  compared  with  the 
first RBMPs. For groundwater, conceptual models together with hydrogeological models and 

expert judgement were used. 

34 

 
Several  of  the  national  types  for  Estonia  in  all  of  the  RBDs  do  not  appear  to  have 

corresponding  intercalibration  types;  three  coastal  water  body,  five  lake  water  body  and  two 
river water body types. 

Partial progress has been made on this recommendation.  

 

Recommendation:  Finalise  the  setting  of  all  reference  conditions  for  the  purpose  of 
the  second  RBMP;  any  gap  (i.e.  lake  diatoms)  should  be  explained  in  the  second 

RBMPs. 

Assessment: Type-specific reference conditions have been established for some or all relevant 

biological quality elements and all physicochemical quality elements. Type-specific reference 
conditions do not appear to have been established for hydromorphological quality elements in 

rivers but have been established for 50 % of types in lakes. Therefore there still appears to be 
some gaps in the setting of all reference conditions.  

 

Recommendation:  Improve 

the  assessment  of  hydromorphological  significant 

pressures taking into account all significant alterations, e.g. drainage, infrastructure, 
barriers etc.     

Assessment:  Significant  hydromorphological  pressures  have  been  taken  into  account  in  the 
reporting  of  significant  pressures  and  account  for  24  %  in  total.  However,  there  are  some 

specific categories that have been excluded from the assessment, including: Physical alteration 
of  channel/bed/riparian  area/shore  –  Navigation,  Dams,  barriers  and  locks  –  Navigation, 

Hydrological  alteration  –  Transport,  Hydrological  alteration  –  Aquaculture,  and 
Hydromorphological alteration - Physical loss of whole or part of the water body. No reasons 

for  these  exclusions  are  provided  in  the  RBMPs.  Generally  the  assessment  of  pressures  on 
surface  waters  for  the  second  RBMP  uses  more  quantitative  data  and  is  specific  to  water 

bodies. The recommendation has partially been fulfilled. 

 

Recommendation:  Cover  diffuse  sources  in  the  inventory  of  pollution  sources 
elaborated  in  the  second  RBMPs  to  the  highest  extent  possible  (e.g.  agricultural 

sources of cadmium, pesticides; storm water run-off, etc.).  

Assessment:  Estonia  reported  that  35  of  the  41  Priority  Substances  and  groups  of  Priority 

Substances were included in the inventories for each RBD. The reasons for the inventory not 
being complete for all Priority Substances and pollutants are presented in the Annex 2 of the 

RBMPs.  It  was  reported  that  the  information  on  substances  not  included  was  insufficient 
during the reference period (2008-2010).  

35 

 
The inventory itself is not available in the main reports of the RBMPs (probably because of the 

large file size), instead it is available on the website of the Ministry of the Environment.  

For  many  substances,  only  point  sources  have  been  considered  when  establishing  the 

inventory, while diffuse sources were not considered. 

This recommendation has not been fulfilled.  

 

Recommendation: Estonia needs to complete the identification of sources of chemical 
pollution, to enable effective measures to be put in place to reduce chemical pollution 

for  Priority  Substances,  and  other  pollutants,  and  then  progressively  reduce  and 
phase-out priority hazardous substances where relevant. 

Assessment: As regards the completion of the inventories of emissions, and the sources taken 
into account, see recommendation above.  

While  not  all  substances  are  included  in  the  inventories,  and  not  all  sources  were  taken  into 

account,  the  Priority  Substances  and  other  substances  identified  as  causing  failure  of  good 
chemical status have been reported, as well as measures to tackle these substances to achieve 
good status by 2021. The indicator gap is reported to be zero (i.e. good status will be reached 

by 2021) for all substances.  

This recommendation has been partially fulfilled 

Topic  3  Monitoring,  assessment  and  classification  of  ecological 
status in surface water bodies 

3.1.  Assessment of implementation and compliance with WFD requirements 

in second RBMPs 

3.1.1.  Monitoring of ecological status/potential 

Monitoring programmes 

Article 8(1) of the WFD requires Member States to establish monitoring programmes for the 
assessment of the status of surface water and of groundwater in order to provide a coherent and 

comprehensive overview of water status within each RBD.  

36 

 
 
Separate  operational  and  surveillance  monitoring  programmes  were  reported  for  each  RBD, 

though the operational programme for the Koiva RBD was reported not to be relevant to any 
water category. The operational programme in the West Estonian RBD did not include lakes 

even though such water bodies were delineated in this RBD.  

Monitoring sites  

Table  3.1  gives  the  number  of  sites  used  for  different  purposes  for  the  second  RBMPs  and 
Table  3.2  compares  the  number  of  monitoring  sites  used  for  surveillance  and  operational 

purposes from the first to the second RBMPs. 

Table  3.2  shows  that  there  are  many  more  monitoring  sites  included  in  the  surveillance 

monitoring programme than in the operational monitoring programme for rivers and lakes.  

Table 3.1 

Number  of  monitoring  sites  in  relevant  water  categories  used  for  different 

purposes in Estonia.  

Monitoring Purpose 

Lakes 

Rivers 

Coastal 

Territorial 

OPE - Operational monitoring 

SUR - Surveillance monitoring 

Total sites irrespective of purpose 

7 

360 

367 

72 

315 

387 

34 

128 

162 

0 

10 

10 

Source: WISE electronic reporting  

37 

 
 
 
 
Table 3.2 

Number of sites used for surveillance and operational monitoring in Estonia 

for the second and first RBMPs. Note that for reasons  of comparability with 
data reported for the first plans, the data for the second RBMPs does not take 

into account whether sites are used for ecological and/or chemical monitoring 

Rivers 

Lakes 

Coastal 

Territorial 

Surv. 

Op 

Surv. 

Op 

Surv 

Op. 

Surv. 

Op. 

Second RBMP  

EE_1 

EE_2 

EE_3 

Total by type of site 

182 

129 

4 

315 

Total number of monitoring sites 

387 

First RBMP 

EE_1 

EE_2 

EE_3 

Total by type of site 

101 

84 

4 

189 

50 

22 

0 

72 

26 

56 

1 

83 

102 

231 

27 

360 

36 

65 

8 

109 

0 

7 

0 

7 

121 

7 

0 

128 

24 

10 

0 

34 

0 

0 

0 

10 

367 

162 

10 

2 

26 

0 

28 

47 

8 

0 

55 

0 

0 

0 

0 

0 

0 

0 

0 

5 

5 

0 

0 

0 

0 

0 

0 

Total number of monitoring sites 

272 

137 

55 

0 

Source: Member States electronic reports to WISE. 

Overall  in  Estonia  there  were  significant  increases  in  the  number  of  surveillance  monitoring 
sites in coastal waters (55 to 128 sites), lakes (109 to 360 sites) and rivers (189 to 315 sites) 
from  the  first  to  the  second  RBMPs.  10  monitoring  sites  were  also  reported  for  territorial 

waters for the second RBMPs.  In contrast  there  were decreases in  the number of operational 
monitoring sites in lakes (28 to 7 sites) and rivers (83 to 72 sites). There were no operational 

monitoring  sites  in  coastal  waters  in  the  first  plans  but  in  the  second  plans  34  sites  were 
reported. No operational monitoring sites were reported in lakes in the Western Estonian and 

Koiva  RBDs,  and  in  rivers  in  the  Koiva  RBD,  in  spite  of  significant  pressures  on  the  water 
bodies in these categories and RBDs having been reported, and some water bodies being at less 

than good status/potential. 

Figure  3.1  shows  the  percentage  of  water  bodies  included  in  surveillance  and  operational 

monitoring in Estonia for the first RBMPs and second RBMPs.  

38 

 
 
  
  
  
  
  
 
 
 
 
  
  
  
  
 
 
 
 
Figure 3.1 

Percentage  of  water  bodies  included  in  surveillance  and  operational 

monitoring in Estonia for the first RBMPs (2010) and second RBMPs (2016). 
Note  no  differentiation  is  made  between  water  bodies  included  in  ecological 

and/or chemical monitoring.  

Source: WISE electronic reporting  

Overall in Estonia the number of delineated coastal, lakes and river water bodies remained the 

same  between  the  two  plans,  though  there  were  small  increases  (one  water  body)  and 
equivalent decreases in the numbers delineated in some RBDs and water categories. All coastal 

water bodies were included in surveillance monitoring for both plans. A smaller proportion of 
lakes and a larger proportion of rivers were included in surveillance monitoring for the second 

RBMPs  compared  to  the  first.  For  the  first  plan  no  coastal  water  bodies  were  included  in 
operational monitoring, while for the second plan 31 % were included. However, there was a 

significant  decrease  in  the  proportion  of  lake  water  bodies  (15  %  to  3  %)  and  river  water 
bodies (11 % to 5 %) included in operational monitoring for the second RBMP compared to 

the first. 

Figure 3.2 shows the proportion of water bodies in  each ecological  status/potential class that 

are included in surveillance monitoring in Estonia. For coastal water bodies (there are none at 
high status) all water bodies in each class are monitored.  

39 

 
 
Figure 3.2 

Proportion  of  water  bodies  in  each  ecological  status/potential  class  that  are 

included  in  surveillance  monitoring  in  Estonia.  Note:  Standard  colours  and 
class  descriptors  for  ecological  status  based  on  WFD  Annex  V,  Article 

1(4)2(I) used for illustration purposes. 

Source: WISE electronic reporting A differentiated presentation between ecological status and potential and 
including all types of quality element can be viewed here - 

https://tableau.discomap.eea.europa.eu/t/Wateronline/views/WISE_SOW_QualityElement_Status_Compare/SWB
_QualityElement_Group?iframeSizedToWindow=true&:embed=y&:display_count=no&:showAppBanner=false

&:showVizHome=no 

In two RBDs (West-Estonian and Koiva) no lakes in less than good ecological status/potential 
were included in operational monitoring, and in the Koiva RBD none of the three river water 

bodies in less than good status/potential were included in operational monitoring.  

Water  bodies  with  a  poor  or  bad  status  in  the  last  two  years  were  selected  for  monitoring. 
Water bodies for which required measures are known or being already implemented to achieve 
the  necessary  status  were  excluded,  according  to  information  in  the  RBMPs10.    This  would 
indicate that there is no control of the efficiency of measures, and no follow up of the gradual 
improvement towards good status11. 

10 Annex 3: River basin monitoring programme 2016-2021 
11  Estonia  subsequently  explained  that  water  bodies  where  good  status  has  been  achieved  and  those  where 
measures  are  still  in  progress  are  not  included  in  the  operational  monitoring  programmes.  The  effectiveness  of 
implemented measures will be assessed by including the relevant water bodies in operational monitoring after the 
necessary measures have been implemented.  

40 

 
 
                                                      
Most lake water bodies in each class are monitored. For rivers, all water bodies in bad status 

are  monitored,  as  well  as  72  %  in  poor  status,  whereas  50  %  or  less  river  water  bodies  in 
moderate, good or high status are monitored. 

Quality elements monitored (excluding River Basin Specific Pollutants) 

Table 3.3 shows the quality elements used for the monitoring of lakes and rivers for the second 

RBMPs; no differentiation is made between purposes of monitoring. 

For  the  first  RBMPs  all  relevant  quality  elements  (biological,  general  physicochemical  and 
hydromorphological)  were  being  monitored  in  rivers  but  for  lakes  and  coastal  waters  some 

quality  elements  were  missing  (phytobenthos  in  some  lake  types;  morphological  conditions 
and tidal regime in coastal waters). 

For  the  second  RBMPs  macroalgae  and  angiosperms  are  not  monitored  in  coastal  waters 
though  phytobenthos  (normally  associated  with  rivers  and  lakes)  are  reported  to  be 
monitored12.  Morphological  conditions  are  not  monitored  and  all  required  general 
physicochemical quality elements are monitored in coastal waters. All relevant biological and 

general  physicochemical  quality  elements  are  reported  to  be  monitored  in  lakes  but 
relevant  biological  and  general 
morphological  conditions  are  not  monitored.  All 

physicochemical  quality  elements  are  reported  to  be  monitored  in  most  rivers  but 
morphological conditions are not monitored at all in any of them. In addition, macrophytes are 

not  monitored  in  two  of  the  three  RBDs  with  rivers.  The  proportion  of  river  water  bodies 
monitored  for  the  different  biological  quality  elements  is  low  (20-30  %),  while  it  is  much 

higher in lakes and coastal waters (50-100 %). 

Table 3.3 

Quality  elements  monitored  for  the  second  RBMPs  in  Estonia  (excluding 

River  Basin  Specific  Pollutants).  Note:  quality  elements  may  be  used  for 
surveillance and/or operational monitoring 

n
o
t
k
n
a
l
p
o
t
y
h
P
Yes 

Yes 

Yes 

s
e
t
y
h
p
o
r
c
a

M

Yes 

Yes 

Biological quality elements 

s
o
h
t
n
e
b
o
t
y
h
P

Yes 

Yes 

Yes 

s
m
r
e
p
s
o
i
g
n
A

e
a
g
l
a
o
r
c
a

M

 (Yes) 

No (Yes)  No (Yes) 

c
i
h
t
n
e
B

s
e
t
a
r
b
e
t
r
e
v
n
i

Yes 

Yes 

Yes 

h
s
i
F

Yes 

Yes 

s
e
i
c
e
p
s

r
e
h
t
O

Lakes 

Rivers 

Coastal 

12 Estonia subsequently clarified that this is a reporting error. 

41 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                      
Hydromorphological quality elements 

e
m
i
g
e
r

l
a
d
i
t

l
a
c
i
g
o
l
o
r
d
y
H

r
o
Yes 

Yes 

Yes 

y
t
i
u
n
i
t
n
o
C

s
n
o
i
t
i
d
n
o
c

l
a
c
i
g
o
l
o
h
p
r
o
M

s
n
o
i
t
i
d
n
o
c

No (Yes) 

No (Yes)  No (Yes) 

No 

Lakes 

Rivers 

Coastal 

General physicochemical quality elements 

y
c
n
e
r
a
p
s
n
a
r
T

s
n
o
i
t
i
d
n
o
c

Yes 

Yes 

Yes 

l
a
m
r
e
h
T

s
n
o
i
t
i
d
n
o
c

Yes 
No 

No 

n
o
i
t
a
n
e
g
y
x
O

s
n
o
i
t
i
d
n
o
c

Yes 

Yes 
No 

y
t
i
n
i
l
a
S

s
n
o
i
t
i
d
n
o
c

No 

No 

Yes 

n
o
i
t
a
c
i
f
i
d
i
c
A

s
u
t
a
t
s

Yes 

Yes 
No 

n
e
g
o
r
t
i

N

s
n
o
i
t
i
d
n
o
c

Yes 

Yes 

Yes 

s
u
r
o
h
p
s
o
h
P

s
n
o
i
t
i
d
n
o
C

Yes 

Yes 

Yes 

e
t
a
c
i
l
i
S

Yes 

No 

Yes 

r
e
h
t
O

d
n
a
n
i
m
r
e
t
e
d

t
n
e
i
r
t
u
n

r
o
f

s
n
o
i
t
i
d
n
o
c

No (Yes) 

No (Yes) 

No 

Lakes 

Rivers 

Coastal 

Source: WISE electronic reporting  Estonia subsequently noted that additional monitoring should have been 
reported. The missing quality elements are shown in brackets. 

In the surveillance monitoring programme for coastal waters, there are no water bodies where 
all the required biological quality elements are included.13 However, for rivers and lakes, the 
situation  seems  better  with  65-70  %  of  the  water  bodies  monitored  for  all  the  required 
biological  quality  elements.  None  of  the  water  bodies  included  in  surveillance  monitoring  in 

any category or RBD was monitored for all the required hydromorphological quality elements. 
63 % of lake water bodies included in surveillance monitoring were monitored for all required 

physicochemical  quality  elements,  but  this  is  not  the  case  for  any  of  river  water  bodies 
included in surveillance monitoring. 

For  operational  monitoring,  three  biological  quality  elements  were  used  in  coastal  waters: 

invertebrates,  while  phytoplankton,  benthic 
phytoplankton,  phytobenthos  and  benthic 
invertebrates and fish were used in lakes. The predominantly used biological quality element in 

rivers was benthic invertebrates, followed by phytobenthos and fish. 

The frequency of monitoring was not in line with the minimum recommended frequencies for 
almost  all  monitored  water  bodies  for  the  different  biological  quality  elements  in  rivers  and 

13 Estonia subsequently clarified that this is a reporting error. It is planned to monitor coastal waters for all quality 
elements, although the monitoring contracts are still ongoing, so it is not clear what was already in place for the 
second RBMPs. 

42 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                      
coastal waters. This was better for lakes, where 20-30 % of the monitored water bodies had at 

least the minimum recommended frequencies for the different biological quality elements.  

River Basin Specific Pollutants and matrices monitored 

Estonia  did  not  report  at  the  generic  quality  element  level  whether  River  Basin  Specific 
Pollutants are monitored; however, information was reported at the site level on which specific 

chemical substances are monitored. 

Member  States  were  not  asked  explicitly  to  report  in  their  electronic  reports  to  WISE  which 

specific  River  Basin  Specific  Pollutants  had  been  identified  or  which  ones  are  specifically 
monitored. The information on which ones are monitored in surface waters was obtained from 

the reported monitored chemical substances that are not Priority Substances: it is assumed that 
these are River Basin Specific Pollutants. On this basis 117 River Basin Specific Pollutants14 
were  reported  to  be  monitored  in  Estonia  as  a  whole:  18  substances  in  fish,  52  in  settled 
sediment  and  116  in  water.  They  were  monitored  in  coastal,  lake,  river  and  also  territorial 
waters  (Table  3.4).  However,  more  than  90  %  of  all  water  bodies  are  not  assessed  for  River 

Basin Specific Pollutants, and more than 85 % are not monitored for these substances.  

Environmental quality standards are developed only for water, and not for sediment or biota. It 

is unclear how other monitored River Basin Specific pollutants are assessed in the absence of 
Environmental Quality Standards. 

Table 3.4 

Number  of  sites  used  to  monitor  River  Basin  Specific  Pollutants  reported  in 
the second RBMPs and non-priority specific pollutants and/or other national 

pollutants  reported  in  the  first  RBMPs  in  Estonia.  Note  the  data  from  both 
cycles may not be fully comparable as different definitions were used and also 

not all Member State reported information at the site level meaning that there 
were no equivalent data for the first RBMPs 

RBMP 

second  

Sites used to monitor River Basin Specific 
Pollutants 

first  

Sites used to monitor non-priority specific 
pollutants and/or other national pollutants 

Lakes 

Rivers 

Coastal 

Territorial 

94 

ND 

140 

ND 

47 

ND 

0 

ND 

Sources: WISE electronic reporting ND = no data 

14  Estonia  subsequently  stated  that  there  are  31  River  Basin  Specific  Pollutants  in  Estonia.  All  of  them  are 
monitored in water and some are monitored also in fish/sediment for background information. 

43 

 
 
                                                      
The analytical methods used were reported to comply with the requirements of Article 4(1) of 
Directive 2009/90/EC15 for all substances monitored for which there are environmental quality 
standards.  

Annex  V  of  the  WFD  provides  guidance  on  the  frequency  of  monitoring  of  the  different 
quality  elements:  once  every  three  months  is  recommended  for  “other  pollutants”  which  are 

taken  here  to  equate  to  river  basin  specific  pollutants.  Surveillance  monitoring  should  be 
carried  out  for  each  monitoring  site  for  a  period  of  one  year  during  the  period  covered  by  a 

RBMP i.e. six years. For river basin specific pollutants this should be done four times for the 
surveillance year, and for operational monitoring four times a year for each year of the cycle. 

Of  the  109  River  Basin  Specific  Pollutants  included  in  surveillance  monitoring,  two  were 
monitored  at  least  at  the  recommended  minimum  frequency  at  all  sites  where  they  were 

monitored,  while  for  85  pollutants  no  sites  were  monitored  at  least  at  the  minimum 
recommended  frequency.  Of  the  46  River  Basin  Specific  Pollutants  included  in  operational 

monitoring, none were monitored at least at the recommended minimum frequency at all sites 
where they were monitored, and for 37 pollutants none of the monitoring sites were. 

Annex  V,  section  1.3.4  of  the  WFD  does  not  explicitly  define  the  matrices  to  which  the 
minimum  recommended  frequency  of  monitoring  of  River  Basin  Specific  Pollutants  (“Other 

Pollutants”)  applies.  Recommended  monitoring  frequencies  are  specified  for  Priority 
Substances in biota and sediment in Article 3(2)(c) of EQS Directive 2008/105/EC: this is once 

per  year  for  operational  and  surveillance  monitoring  purposes.  For  consistency  this 
recommended  frequency of once per  year has been applied to  the monitoring of River  Basin 

Specific Pollutants in biota/sediment.  

Of the 18 River Basin Specific Pollutants monitored in fish, none were sampled at least at the 

recommended frequency at all sites where they were monitored, and for one substance it was at 
none of the sites. Of the 52 River Basin Specific Pollutants monitored in settled sediment, two 

were sampled at least at the required frequency at all sites where they were monitored, while 
for 49 substance it was at none of the sites. 

Transboundary surface water body monitoring 

No monitoring sites were reported to be associated with international monitoring networks. 

15  Commission  Directive  2009/90/EC  of  31  July  2009  laying  down,  pursuant  to  Directive  2000/60/EC  of  the 
European Parliament and of the Council, technical specifications for chemical analysis and monitoring of water 
status https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32009L0090 

44 

 
                                                      
Use of monitoring results for classification 

For coastal waters, the classification of all biological quality elements was based on monitoring 
results,  and  the  number  of  classified  water  bodies  was  the  same  as  the  number  directly 

monitored.  For  the  general  physicochemical  quality  elements,  the  number  of  water  bodies 
classified based on monitoring was also the same as those directly monitored. However, only 

three of these quality elements (transparency, phosphorus and nitrogen) were classified, while 
also  oxygen,  salinity,  pH  and  silicate  were  monitored,  but  not  classified.  The 

hydromorphological  quality  elements  were  not  classified  in  coastal  waters,  but  hydrological 
and tidal regimes were monitored for some water bodies. River Basin Specific Pollutants were 

not classified, even though some were monitored in coastal waters. 

For lakes and rivers, the situation was different, with many mismatches between the number of 

water bodies classified reported to be based on monitoring and the number directly monitored. 
These mismatches mainly show more classified water bodies based on monitoring than those 

directly monitored for almost all the biological and hydromorphological quality elements. This 
is especially apparent  for macrophytes and continuity in rivers, and for morphology in lakes. 

The  RBMPs  indicate  that  classification  has  sometimes  been  based  on  older  monitoring  data, 
which may explain these mismatches. Conversely, some biological quality elements have been 

directly monitored but not classified, such as phytobenthos and fish in lakes and phytoplankton 
in rivers. The same applies to some general physicochemical quality elements, such as oxygen 

in  lakes,  and  to  hydrology  in  lakes.  The  RBMPs  indicate  that  this  monitoring  is  done  to 
provide  a  better  basis  for  developing  classification  methods,  which  are  missing  for  those 

quality elements. For the general physicochemical quality elements nitrogen and phosphorus, a 
large  proportion  (~60%)  of  the  river  water  bodies  is  classified  based  on  expert  judgement. 

Finally, for River Basin Specific Pollutants, 2 % of lake and 10 % of river water bodies were 
classified based on monitoring results. 

3.1.2.  Ecological Status/potential of surface water  

The  ecological  status/potential  of  surface  water  bodies  in  Estonia  for  the  second  RBMPs  is 
illustrated in Map 3.1.  
All water bodies have been classified, except one heavily modified river in the East-Estonian 

RBD.  The  proportion  of  water  bodies  reported  to  be  in  good  or  better  ecological  status  or 
potential  is  60  %  for  rivers,  67  %  for  lakes  and  13  %  for  coastal  waters.  The  overall 

distribution  of  ecological  status/potential  classes  for  all  water  categories  combined  are  given 
for each RBD in Map 3.1. The proportion of water bodies in good or better status is almost the 

same (60 %) in the two large RBDs (West-Estonian and East-Estonian), while it is higher (75 
%) in the smaller Koiva RBD. 

45 

 
Map 3.1 

Ecological status or potential of surface water bodies in Estonia  

High 

Good 

Moderate 

Poor  

Bad 

Unknown 

River Basin Districts 

Countries outside the European 
Union 

Source: WISE, Eurostat (country borders) 
Note: Standard colours based on WFD Annex V, Article 1.4.2(i). 
A differentiated presentation of this data between ecological status and potential and including 
all types of quality element can be viewed here - 
https://tableau.discomap.eea.europa.eu/t/Wateronline/views/WISE_SOW_QualityElement_Statu
s_Compare/SWB_QualityElement_Group?iframeSizedToWindow=true&:embed=y&:display_c
ount=no&:showAppBanner=false&:showVizHome=no 

Figure 3.3 shows the confidence in the classification of ecological status/potential. 

46 

050100kmEE1EE2EE3EE 
 
  
  
  
  
  
  
  
  
 
 
Figure 3.3  Confidence  in  the  classification  of  ecological  status  or  potential  of  surface 

water bodies in Estonia based on the most recently assessed status/potential 

Source: WISE electronic reporting  

The confidence in classification of ecological status is given as high or medium for most lakes 
and coastal waters water bodies, but low for a larger proportion of river water bodies (62 %). It 

should be noted that the confidence in classification is reported as low for most of the water 
bodies classified to be in good ecological status or potential, while the confidence is reported 

as high for most of the water bodies classified to be in moderate or poor ecological status or 
potential (Figure 3.3).  

Information in the RBMPs indicated that the confidence of the status assessment is based on 
the  quality  of  the  data  and  the  length  of  the  period  covered  by  the  data,  the  spatial 

representativeness  of  the  monitoring  program  and  the  variability  of  the  results  of  the 
assessment  of  the  different  quality  elements.  The  actual  criteria  used  to  assess  confidence  as 

described in the RBMPs.  

No  information  has  been  found  in  the  RBMPs  concerning  plans  to  improve  the  level  of 
confidence  and  precision  in  the  classification  of  ecological  status.  This  is  a  problem,  in 

particular for water bodies in good status, where the large majority has been assessed with low 
confidence (40 % of all surface water bodies in Estonia). There is a risk that the proportion of 

water bodies in  good  ecological  status  is  overestimated because of the low confidence in  the 
classification of most of those water bodies. 

47 

 
 
Figure 3.4 compares the ecological status of surface water bodies for the first plans with that 

for the second RBMPs and that expected by 2015. A higher proportion of water bodies were 
classified as good in the first plans. 

Figure 3.4  Ecological  status  or  potential  of  surface  water  bodies  in  Estonia  for  the 
second  RBMPs,  for  the  first  RBMPs  and  expected  in  2015.  The  number  in 

parenthesis  is  the  number  of  surface  water  bodies  for  each  cycle.  Note  the 
period  of  the  assessment  of  status  for  the  second  RBMPs  was  2006  to  2013. 

The year of the assessment of status for first plans is not known 

Source: WISE electronic reporting 

Member States were asked to report the expected date for the achievement of good ecological 

status/potential. The information for Estonia is shown in Figure 3.5. 

48 

 
 
Figure 3.5  Expected  date  of  achievement  of  good  ecological  status/potential  of  surface 

water  bodies  in  Estonia.  The  number  in  the  parenthesis  is  the  number  of 
water bodies in each category 

Source: WISE electronic reporting  

Most of the water bodies in Estonia (63 %) were expected to achieve good ecological status or 

potential by 2015, while the proportion reported to be in good status or potential in the second 
plans is 59 % based on data before 2013 (Figure 3.4). The expectations are different for lakes 
than for rivers with 70 % of the lakes expected to achieve good status or potential by 2015, but 

only 62 % of the rivers. Less than 20 % of coastal water bodies were expected to achieve good 
status by 2015.  The remaining water bodies are expected to achieve good status or potential by 

2021 or 2027 (Figure 3.5). No water bodies were reporting as having less stringent objectives 
already achieved. 

Classification of ecological status in terms of each classified quality element 

Figure 3.6 shows the ecological status/potential of the biological quality elements used in the 
classification of lakes and rivers in Estonia.  

In rivers, only nutrients are monitored and classified in a high proportion of water bodies, and 

are reported to be in good or better ecological status for the majority of classified water bodies. 
The macrophytes,  phytobenthos and benthic invertebrates are  also  in  good or better status  in 

49 

 
 
the majority of classified water bodies, but the proportion of classified water bodies is less than 

half of the total number of water bodies. The classification of rivers in good ecological status 
has  low  confidence  for  most  of  the  water  bodies,  which  is  probably  related  to  the  low 

confidence  criteria,  but  also  with  underlying  problems  with  the  nutrients  classification 
methods.  

A high proportion of water bodies are monitored and classified for many biological and general 
lakes  (phytoplankton,  macrophytes  and  benthic 
physicochemical  quality  elements 

in 

invertebrates,  nutrients)  and  coastal  waters  (all  required  biological  quality  elements, 
transparency  and  nutrients).  The  confidence  in  classification  is  high  for  most  of  the  water 

bodies  in  these  water  categories.  In  coastal  waters,  all  the  biological  quality  elements  except 
phytoplankton  are  in  good  or  better  ecological  status  in  the  majority  of  the  classified  water 

bodies. In lakes, all the classified biological quality elements and nutrients are in good or better 
ecological status for the majority of the classified water bodies.  

Four biological quality elements were used in the classification of 15 of the 16 coastal water 

bodies: phytoplankton  gave the “worst” status/potential classification with 60 % of classified 
water bodies being in less than good status/potential.  Three biological quality elements were 

used  in  the  classification  of  lakes  with  macrophytes  having  the  largest  proportion  (42  %)  of 
classified  water  bodies  in  less  than  good  status.  For  rivers,  the  ecological  status/potential  in 

terms of the four different biological quality elements shows good or even high status for most 
water  bodies  classified  for  these  elements,  except  for  fish,  which  shows  less  than  good 

status/potential for most (65 %) of the water bodies classified (Figure 3.6). 

50 

 
Figure 3.6  Ecological  status/potential  of  the  biological  quality  elements  used  in  the 

classification of lakes and rivers in Estonia.  

Note  that  water  bodies  with  unknown  status/potential  have  been  excluded 

from the figure 

Source: WISE electronic reporting  

Figure  3.7  compares  the  classification  of  biological  quality  elements  in  terms  of  ecological 
status/potential  for  the  two  cycles.  It  should  be  noted  that  this  comparison  should  be  treated 

with caution as there are differences between the numbers of surface water bodies classified for 
individual elements  from  the first to the second RBMPs. This presents  a mixed picture, with 
phytoplankton and macrophytes showing an increased number of surface water bodies at high 
or good status compared to the first RBMPs and phytobenthos, benthic invertebrates and fish 

showing a reduced number. 

51 

 
 
Figure 3.7  Comparison  of  ecological  status/potential  in  Estonia  according  to  classified 

biological  quality  elements  in  rivers  and  lakes  from  the  first  to  the  second 
RBMPs.  

Source: WISE electronic reporting  

Figure 3.8 and Figure 3.9 show the basis of the classification of ecological status/potential of 

rivers and lakes in Estonia for the second RBMPs. Figure 3.9 shows that a significant number 
of  lake  and  coastal  water  bodies  were  classified  using  hydromorphological  elements. 

Biological  quality  elements  were  used  for  classification  in  the  greatest  proportion  of  river 
water  bodies,  while  River  Basin  Specific  Pollutants  were  generally  not  used  in  the 

classification.  

52 

 
 
Figure 3.8 

The  classification  of  the  ecological  status  or  potential  of  rivers  and  lakes  in 

Estonia using one, two, three or four types of quality element. Note: The four 
types are: biological; hydromorphological, general physicochemical and River 

Basin Specific Pollutants. 

Source: WISE electronic reporting 

Figure 3.9 

The percentage of river and lake water bodies in Estonia where no biological 
quality  element  or  no  hydromorphological  (HYMO)  or  no  general 

physicochemical (PHYSCHEM) or no RBSP (River Basin Specific Pollutant) 
has been used in the classification of ecological status or potential 

Source: WISE electronic reporting 
The basis of the classification of the individual quality elements (by monitoring, grouping or 

expert judgement) is illustrated in Figure 3.10. 

53 

 
 
 
Figure 3.10   Basis  of  the  classification  of  ecological  status/potential  in  Estonia.  The 

percentages are in terms of all waterbodies in each category. 

Source: WISE electronic reporting  

Grouping is not listed as a method for classifying quality elements in any of the RBDs. 

In  summary,  the  ecological  status  for  many  quality  elements  is  reported  as  unknown,  not 
applicable or monitored but not used in a large number of water bodies (especially in rivers). 

In rivers, only nutrients are monitored and classified in a high proportion of water bodies, and 

are reported to be in good or better ecological status for the majority of classified water bodies. 
The macrophytes,  phytobenthos and benthic invertebrates are  also  in  good or better status  in 

the majority of classified water bodies, but the proportion of classified water bodies is less than 
half of the total number of water bodies. The classification of rivers in good ecological status 

54 

 
 
has  low  confidence  for  most  of  the  water  bodies,  which  is  probably  related  to  the  low 

confidence  criteria,  but  also  with  underlying  problems  with  the  nutrients  classification 
methods. 

A high proportion of water bodies are monitored and classified for many biological and general 
lakes  (phytoplankton,  macrophytes  and  benthic 
physicochemical  quality  elements 

in 

invertebrates,  nutrients)  and  coastal  waters  (all  required  biological  quality  elements, 
transparency  and  nutrients).  The  confidence  in  classification  is  high  for  most  of  the  water 

bodies  in  these  water  categories.  In  coastal  waters,  all  the  biological  quality  elements  except 
phytoplankton  are  in  good  or  better  ecological  status  in  the  majority  of  the  classified  water 

bodies. In lakes, all the classified biological quality elements and the nutrients are in good or 
high ecological status/potential for the majority of the classified water bodies.  

The  ecological  status/potential  reported  for  the  different  biological  quality  elements  shows 

good or high status  for  most of the water bodies classified for these elements, except  fish in 
rivers, which shows moderate or worse status for most of the water bodies classified for fish 

(Figure 3.6). 

Assessment methods for the biological quality elements 

The methods reported for the biological quality elements covers almost all the gaps remaining 
from the first RBMPs: macrophytes in rivers, phytobenthos and fish in lakes, and macroalgae 

and angiosperms in coastal waters. However, there are still a few remaining gaps. These are:  

  Rivers: The reference conditions of fish in large rivers (Narva River) are not described 
and  there  is  no  indicator  of  status  assessment.  The  indicator  of  the  large  river 

phytoplankton  is  reported  to  be  under  development.  For  macrophytes,  there  is  a 
method, but the class boundaries are currently not intercalibrated. Reference conditions 

for benthic invertebrates may require corrections for some types.  

  Lakes:  For  fish,  the  development  of  an  indicator  for  small  lake  fish  is  reported  to  be 
underway,  the  development  of  indicators  reflecting  the  fish  status  of  the  very  large 

lakes  Võrtsjärv  and  Lake  Peipus  will  begin  in  the  near  future.  The  indicator  for 
phytoplankton in the Lake Võrtsjärv needs to be corrected and the indicator for littoral 
benthic invertebrates of the Peipus shore has been developed, but not yet implemented. 

  Coastal waters: Class boundaries for indicators for phytoplankton, benthic invertebrates 

and phytobenthos methods in the Gulf of Riga are not intercalibrated. 

55 

 
The  sensitivity  of 

the  different  biological  quality  element  methods 

to  different 

pressures/impacts are reported and consistent with the reported impacts: Phytoplankton and the 
benthic aquatic flora (macrophytes, phytobenthos, macroalgae and angiosperms) are sensitive 

to  nutrients.  Benthic 
hydromorphological impacts. Fish is sensitive to nutrients and hydromorphological impacts. 

to  nutrients,  organic  pollution  and 

invertebrates  are  sensitive 

Intercalibration of biological quality element methods  

Only  half  of  the  national  types  are  linked  to  a  common  intercalibration  type.  No  explicit 

information  has  been  provided  in  the  RBMPs  or  background  documents  regarding  the 
approach  used  to  translate  the  results  from  the  common  intercalibrated  types  to  all  other 

national  types.  There  are  also  some  mismatches  between  certain  typology  factors  for  the 
national types and the intercalibration types to which they are linked, such as humic substances 

and  size  for  rivers  and  exposure  for  coastal  waters.  Biological  methods  for  macrophytes  and 
fish  in  rivers  have  not  yet  been  intercalibrated,  according  to  the  RBMPs  and  background 

documents. 

Assessment methods for hydromorphological quality elements 

Hydrological  or  tidal  regime  is  not  assessed  in  terms  of  ecological  status/potential  in  rivers, 

lakes  and  coastal  waters.  The  morphological  conditions  of  lakes  and  coastal  waters  (but  not 
rivers) are reported to be assessed in terms of ecological status/potential and the classification 

boundaries  are  related  to  the  class  boundaries  for  the  sensitive  biological  quality  elements. 
River  continuity  is  assessed  in  terms  of  ecological  status/potential  and  the  classification 

boundaries are related to the class boundaries for the sensitive biological quality elements. 

Hydrological conditions are monitored in some rivers and lakes. According to the RBMPs), the 

reference conditions for the hydromorphological assessment methods are not properly linked to 
the  sensitive  biological  quality  elements  in  a  number  of  water  bodies  assumed  to  be  in 

reference conditions.  

Assessment methods for general physicochemical quality elements 

Nutrient and oxygenation conditions and acidification status are assessed in terms of ecological 
status/potential in in all three water categories and the classification boundaries are related to 

the  class  boundaries  for  the  sensitive  biological  quality  elements.  The  same  applies  to 
transparency  conditions  in  lakes  and  coastal  waters.  Thermal  condition  in  all  three  water 

categories and salinity in coastal waters are also assessed in terms of ecological status/potential 

56 

 
but their classification is not related to the class boundaries for the sensitive biological quality 

elements. 

Standards were reported for 9 general physicochemical quality elements in rivers indicative of 

oxygenation  conditions,  acidification  status  and  nutrient  conditions,  12  in  lakes  indicative  of 
transparency,  oxygenation  conditions,  acidification  status  and  nutrient  conditions  and  5  in 

coastal  waters  indicative  of  transparency  conditions,  acidification  status  and  nutrient 

conditions. All were reported to be consistent with the good‐moderate status boundary of the 
relevant sensitive biological quality elements. 

The standards for general physicochemical quality elements have the same range of values for 
all water categories and all types. The nutrient standards for total phosphorus are close to the 

saturation level for nutrient sensitive biological quality elements (0.1 milligrams per litre) but 
they  are  still  indicated  to  support  good  status  for  these  biological  quality  elements,  based  on 

the  reporting  in  WISE.  Based  on  information  provided  in  the  RBMPs,  however,  the  general 
physicochemical  standards  are  not  linked  to  the  Good/Moderate  boundary  for  sensitive 

biological quality elements. It has been acknowledged that there is a lack of a proper analysis 
of whether the high/good and good/moderate status class boundaries for total nitrogen and total 

phosphorus  correspond  to  the  same  class  boundaries  for  phytobenthos  (diatoms)  and 
macrophytes  in  rivers.  This  analysis  is  stated  to  be  possible  after  the  implementation  of  the 

new monitoring programme. 

Selection of River Basin Specific Pollutants and use of Environmental Quality Standards 

River  Basin  Specific  Pollutants  have  been  identified  based  on  those  identified  in  other 

countries  and  adapted  to  local  conditions  using  expert  judgement.  Substances  from  the  oil 
shale  industry,  such  as  phenols  and  metals  have also  been  identified  as River  Basin  Specific 

Pollutants.  

Environmental Quality Standards were reported for 16 River Basin Specific Pollutants in water 

only.  The  environmental  quality  standards  were  reported  to  be  derived  according  to  the 
Technical  Guidance  Document  No  2716  and  the  analytical  methods  used  for  all  substances 
meet  the  minimum  performance  criteria  laid  down  in  Article  4(1)  of  the  QA/QC  Directive 
(2009/90/EC)17 for the strictest standard applied.  

There is  no information  on how the River Basin  Specific Pollutants were used in  the overall 
classification of ecological status. The environmental quality standard values are reported to be 

16https://circabc.europa.eu/sd/a/0cc3581b-5f65-4b6f-91c6-433a1e947838/TGD-EQS%20CIS-
WFD%2027%20EC%202011.pdf 
17 http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2009:201:0036:0038:EN:PDF 

57 

 
                                                      
both  annual  average  and  maximum  allowable  concentrations  and  are  applicable  at  a  national 

scale. 

Overall classification of ecological status (one-out, all-out principle) 

The  one-out-all-out  principle  has  been  reported  to  be  used  for  the  classification  of  all  water 
bodies, but there is no detailed information on how this was done, for example when some of 

the biological or supporting quality elements have unknown status. 

3.2.  Main changes in implementation and compliance since first RBMPs 

There are a greater number of biological quality element methods developed than in the first 

RBMPs  for  all  water  categories:  macrophytes  in  rivers,  phytobenthos  and  fish  in  lakes, 
macroalgae  and  angiosperms  in  coastal  waters,  many  general  physicochemical  quality 

elements  in  rivers,  lakes  and  coastal  waters,  and  one  hydromorphological  quality  element  in 
rivers (continuity) and lakes (morphology). 

In  general  ecological  status/potential  has  deteriorated  since  the  first  RBMPs  in  terms  of  a 
higher proportion of water bodies in less than good status/potential for the second RBMPs than 

for  the  first  for  all  water  categories  in  all  RBDs,  with  the  exception  of  lakes  in  the  East-
Estonian RBD, where there is  a lower proportion in  less than good status/potential  now than 

for the first plan. 

The  confidence  in  classification  of  ecological  status/potential  has  deteriorated  since  the  first 
RBMPs  for  rivers,  showing  low  confidence  in  62  %  of  the  cases  in  the  second  RBMPs,  in 

contrast to around 45 % in the first RBMPs. 

The proportion of surface water bodies expected to achieve good status/potential after 2015 has 

increased from 20 % in the first plan to 37 % in the second plan. 

A  few  water  bodies  have  changed  class  for  the  biological  quality  elements,  with  changes 
observed  in  both  directions.  However,  for  fish  in  rivers  most  of  the  changes  are  to  a  worse 

class,  while  for  benthic  invertebrates,  most  of  the  changes  are  to  the  better.  None  of  the 
biological  quality  element  changes  are  reported  as  being  consistent,  except  one  lake  in  the 

East-Estonian RBD, where all the biological  quality  elements  show a consistent change. The 
other changes are reported to be due to changes in assessment systems. 

Environmental  quality  standard  values  are  reported  for  water  for  16  River  Basin  Specific 

Pollutants for rivers and lakes. 

58 

 
Overall  in  Estonia  there  were  significant  increases  in  the  number  of  surveillance  monitoring 

sites in coastal waters (55 to 128 sites), lakes (109 to 360 sites) and rivers (189 to 315 sites) 
between the two RBMPs. 10 monitoring sites were also reported for territorial waters for the 

second RBMPs. In contrast there were decreases in the number of operational monitoring sites 
in lakes (28 to 7 sites) and rivers (83 to 72 sites). There were no operational monitoring sites in 

coastal waters in the first plans but in the second plans 34 sites were reported. No operational 
monitoring sites were reported in lakes in the Western Estonian and Koiva RBDs, and in rivers 

in the Koiva RBD, in spite of significant pressures on the water bodies in these categories and 
RBDs having been reported, and some water bodies being at less than good status/potential. 

For  the  first  RBMPs  all  relevant  quality  elements  (biological,  general  physicochemical  and 
hydromorphological)  were  being  monitored  in  rivers  but  for  lakes  and  coastal  waters  some 

quality  elements  were  missing  (phytobenthos  in  some  lake  types;  morphological  conditions 
and tidal regime in coastal waters). 

For  the  second  RBMPs  macroalgae  and  angiosperms  are  not  monitored  in  coastal  waters 

though  phytobenthos  (normally  associated  with  rivers  and  lakes)  are  reported  to  be 
monitored18.  Morphological  conditions  are  not  monitored  and  all  required  general 
physicochemical quality elements are monitored in coastal waters. All relevant biological and 
general  physicochemical  quality  elements  are  reported  to  be  monitored  in  lakes  but 

relevant  biological  and  general 
morphological  conditions  are  not  monitored.  All 
physicochemical  quality  elements  are  reported  to  be  monitored  in  most  rivers  but 

morphological conditions are not monitored at all in any of them. In addition, macrophytes are 
not monitored in two of the three RBDs with  rivers.  Therefore in terms of changes since the 

first  plans  it  seems  that  there  has  been  deterioration  in  the  monitoring  undertaken  with 
morphological conditions not being monitored in any surface water body, and river continuity 

not  monitored  in  rivers.  There  are  still  gaps  in  the  biological  quality  elements  monitored  in 
coastal waters and macrophytes in rivers in two RBDs. 

Overall in Estonia a smaller proportion of lakes and a larger proportion of rivers were included 

in surveillance monitoring for the second RBMPs compared to the first. For the  first plan no 
coastal water bodies were included in operational monitoring, while for the second plan 31 % 

were  included.  However,  there  was  a  significant  decrease  in  the  proportion  of  lake  water 
bodies (15 % to 3 %) and river water bodies (11 % to 5 %) included in operational monitoring 

for the second RBMP compared to the first. 

18 Estonia subsequently clarified that this is a reporting error. 

59 

 
                                                      
3.3.  Progress with Commission recommendations 

  Recommendation: Where there are currently high uncertainties in the characterisation 
of the RBDs, identification of pressures, and in the assessment of status, these need to 

be addressed in the current cycle, to ensure that adequate measures can be put in place 
before the next cycle. The monitoring network was relatively weak, with a low density 

of monitoring stations. 

Assessment:  Overall  in  Estonia  there  were  significant  increases  in  the  number  of 

surveillance monitoring sites in coastal waters (55 to 128 sites), lakes (109 to 360 sites) 
and rivers (189 to 315 sites) from the first to the second RBMPs. 10 monitoring sites 

were also reported for territorial waters for the second RBMPs. In contrast there were 
decreases  in  the  number  of  operational  monitoring  sites  in  lakes  (28  to  7  sites)  and 

rivers (83 to 72 sites). There were no operational monitoring sites in coastal waters in 
the first plans but in the second plans 34 sites were reported19.  

This  recommendation  has  been  partially  fulfilled  as  further  work  is  still  needed  to 
ensure that all quality elements are properly and assessed and that reference conditions 

are set for all biological quality elements. 

  Recommendation:  Estonia  needs  to  develop  chemical  status  monitoring  programmes, 
to  ensure  all  relevant  priority  substances  and  River  Basin  Specific  Pollutants  are 
identified, and that adequate operational and surveillance monitoring is put in place. It 

would be helpful to specify exactly which industrial pollutants are causing failure. 

Assessment:  Details  on  the  monitoring  of  117  River  Basin  Specific  Pollutants  (non 

Priority Substances) for the second plans were reported. However, the methodology for 
the  identification  of  these  River  Basin  Specific  Pollutants  relied  to  a  large  extent  on 

expert judgment. In addition environmental quality standards were derived for only 16 
River Basin Specific Pollutants, and none of them were for biota and sediment, while 

some  River  Basin  Specific  Pollutants  were  monitored  in  these  matrices.  Furthermore, 
most  River  Basin  Specific  Pollutants  were  not  monitored  at  the  WFD  minimum 

recommended frequency. 

It can be concluded that more progress is still needed on this recommendation. 

  Recommendation: There is currently a relatively high proportion of water bodies, both 
groundwater  and  surface  water  bodies  which  are  in  good  or  better  status,  with  the 

exception of the coastal waters that are almost all failing to achieve good status. There 

19  Estonia  subsequently  explained  that  the  criteria  to  define  when  a  site  is  considered  to  be  an  operational 
monitoring site in coastal water have changed over time. For the third  RBMPs the criteria will be harmonised. 

60 

 
                                                      
are also  few unknowns,  despite a monitoring  network which was not  WFD compliant 

for the first RBMPs. Estonia needs to confirm this status assessment through the next 
round  of  surveillance  monitoring  exercises  to  ensure  confidence  in  the  assessment.  A 

WFD compliant surveillance monitoring programme should be in place, the results of 
which should be used to provide the status assessment in the second RBMPs. 

Assessment:  There  has  been  a  significant  increase  in  the  number  of  surveillance 
monitoring sites reported for the second plans. All coastal water bodies were included 

in surveillance monitoring for both the first and second RBMPs s. A smaller proportion 
of lakes were included in surveillance monitoring for the second RBMPs compared to 

the first, while the proportion for rivers increased. There are still significant gaps in the 
quality  elements  (quality  elements)  monitored  for  surveillance  purposes,  e.g. 

morphological conditions and biological quality elements in some water categories and 
RBDs.  In  addition,  there  is  a  very  low  rate  of  alignment  with  the  Annex  V 
recommended  frequencies  for  the  monitoring  of  biological  quality  elements.  For 

example, in terms of the surveillance monitoring of rivers, only 2 % of the water bodies 
monitored for phytobenthos are done so at the recommended frequency, and this is the 

case for only 2 % of water bodies for benthic invertebrates and 6 % for fish.  

It can be concluded that limited progress has been made. 

  Recommendation:  Further  efforts  are  needed  to  ensure  the  monitoring  networks 
become  WFD  compliant,  such  as  to  establish  a  monitoring  programme  for  coastal 
waters, monitoring of all relevant quality elements both in surveillance and operational 

monitoring. 

Assessment:  Overall  in  Estonia  there  were  significant  increases  in  the  number  of 

surveillance  monitoring  sites  in  coastal  waters  (55  to  128  sites)  compared  to  the  first 
RBMPs. There were no operational monitoring sites in coastal waters for the first plan 
but  for the second RBMPs 34 sites  were reported20. For the second plans  macroalgae 
and  angiosperms  are  not  monitored  in  coastal  waters,  though  phytobenthos  (normally 
associated  with  river  and  lakes)  are  reported.  Therefore,  none  of  the  coastal  water 
bodies  included  in  surveillance  monitoring  were  monitored  for  all  required  biological 
quality elements. Morphological conditions were not monitoredand all required general 

physicochemical quality elements were monitored. 

It can be concluded that there has been limited progress on this aspect. 

20  Estonia  subsequently  explained  that  the  criteria  to  define  when  a  site  is  considered  to  be  an  operational 
monitoring site in coastal water have changed over time. For the third RBMPs the criteria will be harmonised. 

61 

 
                                                      
Topic  4  Monitoring,  assessment  and  classification  of  chemical 
status in surface water bodies 

4.1.  Assessment  of 

implementation  and 

compliance  with  WFD 

requirements in second cycle  

4.1.1.  Monitoring of chemical status in surface waters 

Monitoring sites and monitored water bodies used for monitoring of chemical status  

Member  States  have  to  implement  surveillance  and  operational  monitoring  programmes  in 
accordance with the requirements of the WFD and of the EQS Directive for the assessment of 

ecological status/potential and chemical status.  

Surveillance monitoring programmes should allow Member States to supplement and validate 
the  impact  assessment  procedure,  to  efficiently  and  effectively  review  the  design  of  their 
monitoring programmes, and to  assess the long-term  changes in  natural  conditions  and those 

resulting  from  widespread  anthropogenic  activity.  For  operational  purposes,  monitoring  is 
required to establish the status of waterbodies identified as being at risk of failing to meet their 

environmental objectives, and to assess any changes in the status of such waterbodies resulting 
from the PoM. 

Section 3.1.1 of this report summarises the characteristics of the surveillance and operational 
monitoring programmes in Estonia for the second cycle. 

Figure  4.1  summarises  the  proportion  of  sites  used  for  the  monitoring  of  chemical  status  in 

lakes and rivers for the second RBMP. In this figure, no distinction is made between sites used 
for  surveillance  and/or  operational  purposes.  More  detailed  information  can  be  found  on  the 
website of the European Environment Agency21. 

21 https://www.eea.europa.eu/publications/state-of-water 

62 

 
                                                      
Figure 4.1 

Proportion  of  sites  used  for  monitoring  of  chemical  status  and,  for 

comparison, ecological status, in Estonia. The number in parenthesis next to 
the  category  is  the  total  number  of  monitoring  sites  irrespective  of  their 

purpose  

Source: WISE electronic reporting 

A significant proportion of monitoring sites are used for assessment of ecological status (100 

%, 98 %, 80 % and 78 % of sites for lakes, rivers, territorial and coastal waters respectively) 
with a considerably lower proportion of sites used for monitoring of chemical status (26 %, 38 
%, 70 % and 30 % of sites for lakes, rivers, territorial and coastal water respectively).  

Figure 4.2 summarises the proportion of water bodies monitored for chemical status in surface 

waters  for  the  second  RBMP.  In  this  figure  no  distinction  is  made  between  sites  used  for 
surveillance  and/or  operational  purposes.  Also  given  is  the  proportion  of  water  bodies 

monitored for any purpose and, for comparative purpose, those for ecological status. 

63 

 
 
Figure 4.2 

Proportion  of  total  water  bodies  in  each  category  monitored,  monitored  for 

chemical  status  and,  for  comparison,  monitored  for  ecological  status,  in 
Estonia. The number in parenthesis next to the category is the total number of 

water bodies in that category. 

Source: WISE electronic reporting  

Only 16 % of river water bodies were monitored for chemical status, compared with 64 % and 
94 % of lake and coastal  water bodies. All  territorial  waters  are also  monitored for chemical 

status.  

All water bodies failing to achieve good chemical status were reported to be monitored in the 

West-Estonian and East-Estonian RBDs. All water bodies in the Koiva RBD were reported to 
have good chemical status. 

Long-term trend monitoring and monitoring of Priority Substances in water, sediment and 

biota for status assessment 

Monitoring for status assessment 

Requirements 

Article 8.1 of the WFD requires Member States to establish monitoring programmes in order to 

provide  inter  alia  a  coherent  and  comprehensive  overview  of  water  status  within  each  RBD. 
The amount of monitoring undertaken in terms of priority substances, frequency and numbers 

of sites should be sufficient to obtain a reliable and robust assessment of status. According to 
in  2009),  mercury,  hexachlorobenzene  and 
the  EQS  Directive 

(version 

force 

in 

hexachlorobutadiene  have  to  be  monitored  in  biota  for  status  assessment,  unless  Member 

64 

 
 
States  derived  a  standard  for  another  matrix,  which  is  at  least  as  protective  as  the  biota 

standard.  

Spatial coverage 

According to WISE, all Priority Substances, except Total DDT, brominated diphenylethers and 
Trichlorobenzenes  were  reported  to  be  monitored  across  surface  water  bodies  in  the  West-

Estonian and East-Estonian RBDs. (Estonia subsequently clarified that Trichlorobenzenes were 
actually  monitored).  Only  four  substances22  were  monitored  in  the  Koiva  RBD.  All  of  these 
substances are monitored in water. 

In  the  West-Estonian  and  Koiva  RBDs,  no  lake  water  bodies  are  monitored  for  Priority 

Substances  but  in  the  East-Estonian  RBD  95%  of  lake  water  bodies  were  monitored.  In 
contrast,  all  coastal  water  bodies  in  the  West-Estonian  and  50%  in  the  East-Estonian  RBD 
were monitored for more than 10 Priority Substances23. Regarding rivers, 89, 96 and 95% of 
water  bodies  in  the  West-Estonian,  East-Estonian  and  Koiva  RBDs  respectively,  were  not 

monitored for any Priority Substances. Territorial waters were monitored in the East-Estonian 
RBD for more than 10 substances.  

Mercury,  hexachlorobenzene  and  hexachlorobutadiene  are  monitored  in  biota  in  the  West-

Estonian (14 coastal water bodies) and East-Estonian RBDs (one coastal water body) but not in 
the Koiva RBD.  

Frequencies 

The WFD indicates that, for the surveillance and operational monitoring of Priority Substances 

in water, the frequency of monitoring should be at least monthly for one year during the RBMP 
cycle and at least monthly every  year, respectively. Monitoring in biota for status assessment 

should take place at least once every year according to the EQS Directive. In all cases greater 
intervals can be applied by Member States if justified on the basis of technical knowledge and 
expert judgement. 

The  reported  sampling  frequency  in  water  is  at  least  as  high  as  the  recommended  minimum 

frequency for surveillance and operational monitoring for only four Priority Substances (lead, 

22 Estonia subsequently clarified that in the Water Monitoring Programme for the period 2016  – 2021 all RBDs 
will monitor the same list of Priority Substances. 
23 Estonia subsequently clarified that all coastal water bodies are monitored for more than 10 substances. 

65 

 
                                                      
nickel, mercury, cadmium) in rivers. For all other Priority Substances and water categories, the 
reported frequencies are less than the recommended minimum frequency.24 

Monitoring  frequencies  for  mercury,  hexachlorobenzene  and  hexachlorobutadiene  in  biota 

meet the recommended minimum frequency at the majority of monitoring sites. 

Monitoring for long-term trend assessment 

Requirements 

Article 3.3 of the EQS Directive (version in force in 2009) requires Member States to monitor 
14  priority  substances25  that  tend  to  accumulate  in  sediment  and/or  biota,  for  the  purpose  of 
long-term  trend  assessment.  Monitoring  should  take  place  at  least  once  every  three  years, 

unless technical knowledge and expert judgment justify another interval.  

Spatial coverage 

Eleven of the 14 substances are monitored either in sediment and/or biota for trend assessment 
in the East and West Aegean RBDs, and this monitoring is reported to be both for status and 

long-term  trend  assessment.  No  monitoring  in  sediment  or  biota  was  reported  in  the  Koiva 
RBD. 

The  West  Estonian  RBD  and  the  East  Estonian  RBDs  monitored  1026  of  the  14  relevant 
substances  in  sediment  in  respectively  10  and  seven  river  water  bodies.  These  RBDs  also 
monitored  six  of  the  14  substances  in  biota  in  respectively  14  and  one  coastal  water  bodies. 

Monitoring for long-term trend assessment was not undertaken in territorial waters and lakes.  

24 Estonia subsequently that monitoring frequencies in water in the 2016-21 Water Monitoring Programme will be 
four times per year and twice per cycle and in sediment and biota monitoring will be performed once per year and 
twice per cycle. 
25Anthracene, 
hexachlorobenzene,  hexabutadiene,  hexachlorocyclohexane, 
Tributyltin. 
26 Estonia subsequently informed that all 14 Priority Substances will be monitored in sediment for long-term trend 
analysis in the Water Monitoring Programme for 2016-2021, in all three RBDs. 

fluoranthene, 
lead,  mercury,  pentachlorobenzene,  PAH, 

chloroalkanes,  DEHP, 

cadmium,  C10-13 

diphenylether, 

brominated 

66 

 
 
 
                                                      
Frequencies 

Monitoring of biota is undertaken between one and three times per year and from at least once 
to three times per cycle. Monitoring of sediment is undertaken between one and two times per 

year  and  from  at  least  once  to  three  times  per  cycle.  Some  but  not  all  of  these  meet  the 
recommended minimum frequency.27   

Monitoring of Priority Substances that are discharged in each RBD  

Annex  V  of  the  WFD  states,  in  Section  1.3.1  (Design  of  surveillance  monitoring),  that 

“Surveillance monitoring shall be carried out for each monitoring site for a period of one year 
during  the  period  covered  by  a  RBMP  for  [inter  alia]:  priority  list  pollutants  which  are 

discharged into the river basin or sub-basin.” Section 1.3.2 (Design of operational monitoring) 
of the Directive states that “In order to assess the magnitude of the pressure to which bodies of 

surface  water  are  subject  Member  States  shall  monitor  for  those  quality  elements  which  are 
indicative  of  the  pressures  to  which  the  body  or  bodies  are  subject.  In  order  to  assess  the 

impact  of  these  pressures,  Member  States  shall  monitor  as  relevant  [inter  alia]:  all  priority 
substances discharged, and other pollutants discharged in significant quantities.” 

Member States are therefore required to monitor all Priority Substances which are discharged 

into the river basin or sub-basin.  

In  the  West  Estonian  and  East  Estonian  RBDs,  32  Priority  Substances  are  included  in 
inventories. Of these 32, 728 are discharged and 30 are monitored including those discharged29.  

In  the  Koiva  RBD,  32  Priority  Substances  are  in  inventories;  however  none  is  assessed  as 
discharged.  Nevertheless,  four  Priority  Substances  are  monitored:  lead,  mercury,  nickel  and 
cadmium30.  

Performance of analytical methods used  

The  analytical  methods  used  for  all  Priority  Substances  are  reported  to  meet  the  minimum 
performance  criteria  laid  down  in  Article  4(1)  of  Directive  2009/90/EC31  for  the  strictest 
standard applied.  

27  Estonia  subsequently  informed  that  monitoring  frequencies  in  sediment  and  biota  in  the  2016-2021  Water 
Monitoring Programme will be once per year and twice per cycle. 
28 DEHP, Trichloromethane, lead, mercury, nickel, cadmium and chloroalkanes C10-13 
29  Estonia clarified that trichlorobenzene is actually also  monitored (this substance appears  in the inventories as 
not discharged and it is not reported as monitored in WISE). 
30 Estonia have provided additional information stating that since 2016 a new water monitoring programme was 
put in  place and that all priority substances will be monitored in all RBDs as part of this programme.  

67 

 
                                                      
The  method  of  dealing  with  measurements  of  Priority  Substances  lower  than  the  limit  of 

quantification is as specified in Article 5 of Directive 2009/90/EC. 

4.1.2.  Chemical Status of surface water bodies 

Member States  are  required to  report the  year on which the  assessment of chemical  status  is 
based. This  may be the  year that the surface water body was monitored. In case of  grouping 

this may be the year in which monitoring took place in the surface water bodies within a group 
that  are  used  to  extrapolate  results  to  non-monitored  surface  water  bodies  within  the  same 

group.  In  Estonia  as  a  whole  the  chemical  assessments  were  carried  out  in  2014  for  94%  of 
water bodies and with almost all the remaining water bodies assessed in 2012 and 2013. This 

general pattern occurred in the East Estonian and West Estonian RBDs. In the Koiva RBD the 
remaining water bodies were assessed in 2013 only. 

The  chemical  status  of  surface  water  bodies  for  the  second  RBMP  is  illustrated  in  Map  4.1. 
This is based on the most recent assessment of status. 

31  Commission  Directive  2009/90/EC  of  31  July  2009  laying  down,  pursuant  to  Directive  2000/60/EC  of  the 
European Parliament and of the Council, technical specifications for chemical analysis and monitoring of water 
status https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32009L0090  

68 

 
                                                                                                                                                        
Map 4.1 

 Chemical status of surface water bodies in Estonia based on the most recently 

assessed  status  of the  surface  water  bodies  Note:  Standard  colours  based  on 
WFD Annex V, Article 1(4)3.  

Source: WISE, Eurostat (country borders) 

Table 4.1 shows the chemical status of surface waters for the first and second RBMPs.  

69 

GoodFailing to achieve to goodUnknownRiver Basin DistrictsCountries outside the EU 
 
 
 
Table 4.1  Chemical  status  of  surface  water  bodies  in  Estonia  for  the  second  and  first 

RBMPs. Note: the number in parenthesis next to the water category is the number of water 
bodies.  Note:  Chemical  status  assessment  is  based  on  the  standards  laid  down  in  EQS 

Directive 2008/105/EC (version in force on 13 January 2009). Some Member States did not 
implement the Directive in the first RBMPs as the transposition deadline was in July 2010, 

after the adoption of the first RBMPs 

Category 

second RBMP 

Rivers (645) 

Lakes (89) 

Coastal (16) 

Territorial (2) 

Total 

first RBMP 

Rivers (645) 

Lakes (89) 

Coastal (16) 

Total 

Good 

Failing to achieve good 

Unknown 

Number 

% 

Number 

% 

Number 

% 

69 

2 

2 

73 

641 

89 

16 

746 

11% 

2% 

100% 

10% 

99% 

100% 

100% 

99% 

3 

12 

15 

4 

4 

573 

87 

4 

664 

89% 

98% 

25% 

88% 

0.50% 

75% 

2% 

1% 

1% 

0 

0% 

Source: WISE electronic reporting  

Surface water bodies not monitored for chemical status are reported as unknown status. Large 

percentages of surface water bodies are reported to be unmonitored (88-96 % depending on the 
water  category).  In  addition,  not  all  water  bodies  reported  as  monitored  appears  to  be 

classified. 

Figure 4.3 shows the confidence in the classification of chemical status for the second RBMP. 
In  all  RBDs,  the  water  bodies  classified  on  the  basis  of  monitoring  were  classified  with 
medium  confidence.  (Water  bodies  not  monitored  were  not  classified).  Confidence  in  the 

classification of chemical status for the first RBMPs was not reported. 

70 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Figure 4.3  Confidence in the classification of chemical status of surface water bodies in 

Estonia based on the most recently assessed status/potential  

Source: WISE electronic reporting 

Figure  4.4  compares  the  chemical  status  of  surface  water  bodies  reported  in  the  first  RBMP 

with  that  reported  in  the  second  RBMP  (based  on  the  most  recent  assessment  of  status)  and 
that expected by 2015. Between the two RBMPs, there was a large decrease in the proportion 

of surface water bodies with good chemical status from 99 to 10 % and a significant increase in 
the  proportion  with  unknown  status  from  0  to  88  %.  However,  98  %  of  water  bodies  were 

expected to reach good status by 2015. 

The assessment of chemical status reported in the second RBMP was expected to be based on 
the standards laid down in the EQS Directive (version in force on 13 January 200932). Some 
Member  States  did  not  implement  the  Directive  in  the  first  RBMPs  as  the  transposition 

deadline was in July 2010, after the adoption of the first RBMPs. 

32  Directive  2013/39/EU,  which  amended  the  Environmental  Quality  Standards  Directive,  introduced  a  less 
stringent annual average environmental quality standard for naphthalene in transitional waters. This less stringent 
environmental  quality  standard  should  be  taken  into  account  for  the  determination  of  surface  water  chemical 
status by the 2015 deadline laid down in Article 4 of the WFD. 

71 

 
 
 
 
 
                                                      
Figure 4.4  Chemical status of surface water bodies in Estonia for the second RBMP, for 

the  first  plan  and  expected  in  2015.  The  number  in  the  parenthesis  is  the 
number  of  surface  water  bodies  for  both  cycles.  Note  the  period  of  the 

assessment of status for the second RBMP was 2011 to 2014. The year of the 
assessment of status for first RBMP is not known 

Source: WISE electronic reporting  

From  the  figure  above,  it  is  not  entirely  clear  how  so  many  water  bodies  can  be  in  good 

chemical status in 2015, when their status is unknown in the second RBMPs. 

Directive  2013/39/EU  amended  the  EQS  Directive.  In  particular,  it  sets  more  stringent 
environmental  quality  standards  for  seven  substances33.Member  States  were  asked  to  report 
whether  the  new  standards  caused  the  status  of  their  surface  water  bodies  to  appear  to 

deteriorate. This was not the case in Estonia.  

Good  chemical  status  should  be  reached  by  2021  in  relation  to  the  revised  environmental 
quality  standards,  unless  Member  States  apply  exemptions  under  WFD  Article  4(4)  or  less 
stringent objectives under WFD Article 4(5). 

Member States were asked to report the expected date for the achievement  of good chemical 

status. The information is shown in Figure 4.5. All lakes and territorial waters, more than 99% 
of rivers and 19% of coastal waters were expected to be at good chemical status by the end of 

2015 with all water bodies expected to reach Good status by the end of the second cycle. 

33  Anthracene,  Brominated  diphenylether,  Fluoranthene,  Lead  and  its  compounds,  Naphthalene,  Nickel  and  its 
compounds, Polycyclic Aromatic Hydrocarbons (PAH) 

72 

 
 
 
 
                                                      
Figure 4.5  Expected  date  of  achievement  of  good  chemical  of  surface  water  bodies  in 

Estonia. The number in the parenthesis is the number of water bodies in each 
category 

Source: WISE electronic reporting  

Priority Substances causing the failure of good chemical status 

Member States were expected to report exceedances for individual substances on the basis of 
the more stringent 2013 Environmental Quality Standards (see above). 

Four substances are causing failure in 14 waterbodies. These substances are shown in  Figure 
4.6, together with the proportion of surface waterbodies failing for each of them.  

The substance causing the greatest proportion of waterbodies to fail to achieve good chemical 
status  was mercury;  causing failure in  all 12 water bodies, followed by  dichloromethane and 

pentachlorophenol (exceeding their standards in two water bodies each) an nickel (one failure).   

73 

 
 
 
Figure 4.6 

Priority Substances causing failure to achieve good chemical status in surface 

water bodies in Estonia 

Source:  WISE electronic reporting  

Overall for surface water bodies in Estonia, the largest proportion of exceedances was for the 
maximum  allowable  concentration-environmental  quality  standards  for  mercury  (80%  of  the 

exceedances).  There  were  no  exceedances  reported  for  the  annual  average  environmental 
quality standards.  

Ubiquitous persistent, bioaccumulative and toxic Priority Substances 

According  to  article  8(a)  of  the  EQS  Directive34,  eight  priority  substances  and  groups  of 
priority  substances  are  behaving  like  ubiquitous,  persistent,  bioaccumulative  and  toxic 
substances35.  These  substances  are  generally  expected  to  cause  widespread  exceedances,  and 
their emissions can be challenging to tackle (e.g. due to long-range atmospheric transport and 
deposition). In order to show the progress made in tackling other priority substances, Member 

States have the possibility to present the information related to chemical status separately for 
these substances.  

The  influence  of  ubiquitous  persistent,  bioaccumulative  and  toxic  Priority  Substances  on  the 
assessment  of  chemical  status  in  Estonia  is  assessed  by  Estonia  as  limited.  Overall  2  %  of 

surface water bodies fail to achieve good status; 1.6 % of surface waters fail due to one such 
substance  (mercury)  with  the  remainder  failing  due  to  other  substances.  However,  the  true 

34 Amended by Directive 2013/39/EU 
35 Brominated diphenylether, Mercury and its compounds, Polyaromatic hydrocarbons (PAH), Tributyltin,  PFOS, 
dioxins, hexabromocyclodecane and heptachlor 

74 

 
 
                                                      
extent  of  the  influence  of  these  substances  cannot  be  fully  determined  because  a  large 

proportion of surface water bodies (88%) has been assigned an unknown status class because 
they have not been monitored.  

This is illustrated in the 2018 State of Water report of the European Environment Agency36. 

Priority Substances used in the assessment of chemical status compared to those monitored 

All 41 Priority Substances are reported to be used in the assessment of chemical status  in the 
West-Estonian  and  East-Estonian  RBDs.  According  to  WISE  all  these  substances  are 
monitored in each of these RBDs, apart from Trichlorobenzenes (all isomers)37, total DDT and 
brominated diphenylethers.  

In  the  Koiva  RBD,  all  41  Priority  Substances  were  reported  to  be  used  in  the  assessment  of 
status, however only four were monitored (cadmium, lead, nickel, mercury)38. 

Application of alternative environmental quality standards for water, biota and sediment  

According  to  the  EQS  Directive,  Member  States  may  opt  to  apply  environmental  quality 
standards for  another matrix than the one specified in  the Directive for a given substance.  If 

they do so, they have to ensure the environmental quality standard they set in the other matrix 
(or  matrices)  offers  at  least  the  same  level  of  protection  as  the  standard  established  in  the 

Directive. 

According to WISE, Estonia applied 18 of the standards from Annex I of the EQS Directive to 

assess chemical status. Alternative and/or additional standards were reported for the remaining 
Priority  Substances,  in  biota  (including  in  fish)  and  settled  sediment;  these  standards  were 

reported as applied at national scale. It is however unclear how these standards were set. For 
some of the substances for which an additional standard was set, it is also unclear how these 

were  applied  as  in  some  cases  no  monitoring  seemed  to  be  reported  for  the  substance  in  the 
corresponding matrix.  

36https://www.eea.europa.eu/publications/state-of-water  (p40-41  of  the  report).  Also  available  in  a  more 
interactive format at :  
https://tableau.discomap.eea.europa.eu/t/Wateronline/views/WISE_SOW_SWB_Chemical_Status_Maps/SWB_F
ailing_Good_Chemical_Status_RBD?iframeSizedToWindow=true&:embed=y&:showAppBanner=false&:display
_count=no&:showVizHome=no   
37 Estonia subsequently informed that trichlorobenzenes (all isomers) were monitored. 
38 Estonia subsequently informed that from 2016, all Priority Substances were monitored in all RBDs.  

75 

 
                                                      
Use of mixing zones  

Article 4 of the EQS Directive provides Member States with the option of designating mixing 
zones adjacent to points of discharge in surface waters. Concentrations of priority substances 

may exceed the relevant environmental quality standard within such mixing zones if they do 
not affect the compliance of the rest of the surface water body with those standards. Member 

States that designate mixing zones are required to include within their RBMPs a description of 
the  approaches  and  methodologies  applied  to  define  such  zones,  and  a  description  of  the 

measures taken to reduce the extent of the mixing zones in the future. 

Mixing zones have been designated in the West-Estonian and East-Estonian RBDs, but not in 

the  Koiva  RBD.  Where  mixing  zones  have  been  designated,  they  are  reported  to  have  been 
designated following the tiered approach as laid down in the ‘Technical Background Document 
on Identification of Mixing Zones’39. The two RBDs reported that measures have been put in 
place to reduce the extent of the mixing zones.  

Background concentrations and bioavailability 

The  EQS  Directive  stipulates  that  Member  States  have  the  possibility,  when  assessing  the 

monitoring results against the environmental quality standard, to take into account: 

(a)  natural  background  concentrations  for  metals  and  their  compounds,  if  they  prevent 

compliance with the environmental quality standard, and; 

(b) hardness, pH or other water quality parameters that affect the bioavailability of metals. 

None of the three RBDs reported information on whether natural background concentrations or 
bioavailability were taken into account.  

4.2.  Main changes in implementation and compliance since first cycle 

Between the two RBMPs, there appears to  be an increase in  monitoring  sites for operational 

purposes (an increase of three sites) due to  an increase in coastal sites but a decrease in lake 
and  river  sites.  However,  there  has  been  a  decrease  in  the  number  of  surface  water  bodies 

monitored  (a  decrease  of  44)  due  to  a  relatively  large  decrease  in  river  monitoring.  For 
surveillance  monitoring  the  number  of  sites  has  increased  by  544,  and  the  number  of  water 

39https://circabc.europa.eu/sd/a/78ce94bb-6f1c-4379-87ac-
88a18967c4c3/Technical%2520Background%2520Document%2520on%2520the%2520Identification%2520of%
2520Mixing%2520Zones.doc+&cd=1&hl=en&ct=clnk&gl=uk  

76 

 
                                                      
bodies monitored has increased by 51. No  explanation is  available in  the RBMPs to  account 

for these changes.  

The RBMPs acknowledge that the data for monitoring programmes has been uneven over the 

years  and,  in  some  cases,  insufficient  in  terms  of  catchment  areas,  pressures,  population 
density, water volume and water regime, and state that a greater focus should be given to data 

collection when planning the next monitoring program. No explicit information has been found 
in  the  RBMPs  relating  to  transboundary  monitoring  programmes.  Since  there  are  no 

international  RBMPs  for  transboundary  RBDs  in  Estonia,  it  can  be  assumed  that  there  is  no 
transboundary surface water monitoring programme for the monitoring of Priority Substances. 

The reporting of chemical status has changed significantly from the first to second RBMPs. In 

the first RBMPs the chemical status of surface water bodies was assessed using a broad range 
of substances,  not  just Priority Substances, although there was actually little monitoring data 

(data was available mainly for heavy metals, phenols and some plant protection products). In 
the  first  RBMPs,  no  Priority  Substances  were  identified  as  exceeding  their  standards  (only 

phenols – not a priority substance - were failing in the few locations assessed). In the absence 
of  monitoring  data,  expert  judgment  was  used  for  classification  on  the  basis  of  analysis  of 

pressures and applied to all surface water bodies. In the second RBMP, the chemical status was 
assessed  based  on  the  list  of  Priority  Substances.  Monitoring  data  was  gathered  for  a  larger 

number of these substances, in  slightly  less than a quarter of the water bodies. The status  of 
non-monitored water bodies was reported as unknown. These methodological changes, as well 

as the increase in the monitoring data available explain the large decrease in the proportion of 
surface water bodies with good chemical status from 99.5 to 10% and the significant increase 

in the proportion with unknown status from 0 to 88%. 

4.3.  Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first PoM requested action 
on the following: 

  Recommendation: Where there are currently high uncertainties in the characterisation 
of the RBDs, identification of pressures, and in the assessment of status, these need to 

be addressed in the current cycle, to ensure that adequate measures can be put in place 
before the next cycle.  

Assessment: Between the first  and second RBMPs there has been  a large decrease in 

proportion of surface water bodies with good chemical status from 99.5 to 10 % and a 

77 

 
significant  increase  in  the  proportion  with  unknown  status  from  0  to  88  %;  the 

remainder failed to achieve good chemical status. This general pattern occurred across 
all  three  RBDs  and  all  Natural/Heavily  Modified/Artificial  water  body  categories. 

Water  bodies  were  classified  on  the  basis  of  monitoring  data  only,  and  this 
classification was always associated with medium confidence in the assessment. Water 

bodies  not  monitored  were  assigned  unknown  status.  While  there  has  been  some 
progress  with  the  monitoring  of  chemical  status  in  terms  of  the  range  of  Priority 

Substances monitored which has fed into a more robust assessment of chemical status 
compared  to  first  RBMP,  the  spatial  extent  of  the  monitoring  programme  remains 

limited.  This recommendation is partially fulfilled. 

  Recommendation:  Estonia  needs  to  develop  chemical  status  monitoring  programmes, 
to  ensure  all  relevant  Priority  Substances  and  River  Basin  Specific  Pollutants  are 
identified, and that adequate operational and surveillance monitoring is put in place. It 

would be helpful to specify exactly which industrial pollutants are causing failure. 

Assessment:  Progress  with  monitoring  programmes  for  chemical  status  assessment  is 

described in the following recommendations (see below).   

Estonia  has  reported  to  WISE  the  Priority  Substances  causing  failure  in  the  water 

bodies monitored. However, there are 88% of water bodies that are not monitored and 
assigned unknown status; so the full extent of industrial pollutants causing failure may 

be underestimated.  

This recommendation is partially fulfilled. 

  Recommendation:  Mercury,  hexachlorobenzene  and  hexachlorobutadiene  are  not  the 
only  Priority  Substances  for  which  monitoring  in  a  non-water  matrix  (biota  in  these 

three  instances,  with  reference  to  the  biota  standards  in  the  environmental  quality 
standard)  is  appropriate.  The  requirement  for  trend  monitoring  in  sediment  or  biota 

specified for several substances in Article 3(3) of the Environmental Quality Standards 
Directive will also need to be reflected in the next RBMPs. 

Assessment: Mercury, hexachlorobenzene and hexabutadiene were monitored in biota 
for  status  assessment  but  only  in  what  seems  to  be  a  very  limited  number  of  sites  in 

coastal  and territorial waters,  in  two of the three RBDs. The frequency of monitoring 
met the recommended minimum frequency in a majority of monitoring sites. No biota 

monitoring was performed in the Koiva RBD. 

Trend  monitoring  in  sediment  and/or  biota  covered  several  11  of  the  14  required 

Priority  Substances  in  two  of  the  three  RBDs,  and  the  number  of  water  bodies 

78 

 
monitored  appears  to  be  very  limited.  The  monitoring  was  performed  at  the 

recommended minimum frequency at some but not all sites. No trend monitoring was 
reported in the Koiva RBD.40 

This recommendation is partially fulfilled. 

  Recommendation: There is currently a relatively high proportion of water bodies, both 
groundwater  and  surface  water  bodies  which  are  in  good  or  better  status,  with  the 
exception of the coastal waters that are almost all failing to achieve good status. There 

are also  few unknowns,  despite a monitoring  network which was  not  WFD compliant 
for the first RBMPs. Estonia needs to confirm this status assessment through the next 

round of surveillance monitoring exercises to ensure confidence in the assessment.  

Assessment: The chemical status of surface water bodies reported in the second RBMP 

differs significantly from that reported in the first RBMP. In the second RBMP, 10 % 
of  water  bodies  are  in  good  status;  2  %  fail  to  achieve  good  status  and  88  %  are 

unknown status.  

The  methodology  used  for  the  assessment  changed  significantly  between  the  two 

RBMPs. The status assessment in the second RBMP was based on monitoring for the 
12 % of water bodies classified and was assigned medium confidence. Non-monitored 

water bodies were in  unknown status  in  the second RBMP, while in the first  RBMPs 
they were classified based in expert judgment (often as reaching good chemical status). 

Chemical  status  assessment  in  the  second  RBMP  only  considers  priority  substances, 
while other substances were also taken into account in the first RBMP. 

The changes observed in the chemical status also result from the improvements in the 
monitoring  programmes.  Between  the  two  RBMPs,  the  number  of  surveillance 

monitoring  sites  and  water  bodies  monitored  increased,  as  well  as  the  number  of 
priority substances monitored. However, a large number of surface water bodies remain 
unmonitored for Priority Substances.41  

This recommendation is partially fulfilled. 

  Recommendation:  Further  efforts  are  needed  to  ensure  the  monitoring  networks 
become  WFD  compliant,  such  as  to  establish  a  monitoring  programme  for  coastal 

40 Estonia subsequently informed that monitoring for all relevant Priority Substances in sediment and/or biota for 
status and long-term trend assessment started in 2016 in all RBDs and results will be reported in the next RBMP. 
41 Estonia subsequently informed that monitoring programmes will be further enhanced in the 2016-2021 period 
and reported in the next RBMP. 

79 

 
                                                      
waters, monitoring of all relevant quality elements both in surveillance and operational 

monitoring. 

Assessment: See the assessment of the above recommendation for a description of the 

improvements of the monitoring programmes. 

The monitoring programmes reported in the second RBMP for chemical status include 

monitoring  in  all  water  categories.  All  territorial  waters  and  almost  all  coastal  water 
bodies  were  monitored  but  this  was  the  case  for  only  about  20  %  of  inland  water 

bodies. 

39  of  the  41  Priority  Substances  were  monitored  in  water  in  two  of  the  three  RBDs, 
while  monitoring  was  performed  for  only  four  substances  in  the  Koiva  RBD.  All 

substances identified as discharged were monitored (however not all priority substances 
are included in the inventories, so it is unclear whether all discharged substances were 

identified).  The  frequency  of  monitoring  was  lower  than  the  recommended  minimum 
frequencies for a large majority of substances. 

For  an assessment of monitoring performed in  biota for status  assessment,  and of the 
long-term trend monitoring, see the related recommendation above. 

Efforts  have  been  made  to  improve  the  monitoring  programmes  used  to  underpin  the 

assessment  of  chemical  status  but  some  shortcomings  remain.  One  of  the  main 
shortcomings  is  that  the  extent  of  the  monitoring  programme  remain  insufficient  to 

allow classification of all water bodies, in the absence of robust grouping/ extrapolation 
methodologies.  This recommendation is partially fulfilled.  

  Recommendation: Include for the second RBMP Priority Substances in chemical status 

assessment and River Basin Specific Pollutants in ecological status assessment 

Assessment:  All  41  Priority  Substances  (and  not  other  substances)  are  reported  to  be 

used in the assessment of chemical status. This part of the recommendation is fulfilled. 

80 

 
 
Topic  5  Monitoring,  assessment  and  classification  of  quantitative 
status of groundwater bodies 

5.1.  Assessment  of 

implementation  and  compliance  with  the  WFD 

requirements in the second cycle 

5.1.1. Monitoring of quantitative status in groundwater 

Data reported to WISE indicates that there are 39 groundwater bodies in Estonia. According to 

the WISE reporting on monitoring purposes, quantitative monitoring was not carried out in any 
of these groundwater bodies (Table 5.1). In total about 21 % of the groundwater bodies are at 

risk.  However,  the  RBMPs  state  that  all  groundwater  bodies  are  subject  to  quantitative 
monitoring with details given in a Chapter entitled ‘Assessment of quantitative status’42. 

The number of groundwater bodies increased by 50 %, from 26 in the first RBMP to 39 in the 
second  RBMP,  but  the  total  groundwater  body  area  remained  almost  the  same.  Four 

groundwater bodies remained unchanged since the first RBMP. 

The  number  of  monitored  groundwater  bodies  was  24  out  of  26  in  the  first  RBMP  and  the 
number of monitoring sites for quantitative status was 265. For the second RBMP,  Table 5.2 

shows  the  number  of  monitoring  sites  for  quantitative  status  as  reported  in  WISE,  and  the 
number of monitoring sites and their purpose is listed in Table 5.3. Due to missing data and the 

changes  in  delineation  of  groundwater  bodies,  the  quantitative  monitoring  situation  in  the 
second RBMP cannot be assessed or compared to the first RBMP43. 

No  information  was  reported  in  WISE  on  how  many  groundwater  bodies  are  identified  as 
Drinking Water Protected Areas.44 

42 Estonia clarified that quantitative monitoring was in fact carried out in 30 of the 39 groundwater bodies. 
43 Estonia subsequently clarified that 243 monitoring sites were used for quantitative monitoring. 
44 Estonia subsequently clarified that there are 39 Drinking Water Protected Areas. 

81 

 
 
 
                                                      
Table 5.1 

Number  of  water  bodies  in  Estonia  directly  monitored  and  the  purpose  of 

monitoring 

Monitoring Purpose 

Europea
n Union 
RBD 
Code 

Total 
ground-
water 
bodies 
directly 
monitored 

CHE - 
Chemical 
status 

NID - Nutrient 
sensitive area 
under the Nitrates 
Directive - WFD 
Annex IV.1.iv 

OPE – 
Operatio
-nal 
monitor-
ing 

QUA – 
Quantitati
ve status 

EE1 

EE2 

EE3 

16 

20 

3 

0 (16) 

0 

0 (3) 

0 (2) 

0 (3) 

0 

5 

6 

0 

0 (12) 

0 (15) 

0 (3) 

SOE - 
EIONET 
State of 
Environ-
ment 
monitorin
g 

0 (12) 

0 (20) 

0 (2) 

SUR – 
Surveil-
lance 
monitori
ng 

16 

20 

3 

Source: WISE electronic reporting. The numbers in brackets were subsequently provided by Estonia. 

Table 5.2 

Proportion of groundwater bodies in Estonia monitored for quantitative status 

European Union 
RBD Code 

No of groundwater 
bodies with 
quantitative 
monitoring 

Total No. 
groundwater 
bodies 

EE1 

EE2 

EE3 

0 (12) 

0 (12) 

0  

16 

20 

3 

% of total groundwater bodies 
monitored for quantitative status 

0 (75) 

0 (75) 

0  

Source: WISE electronic reporting. The numbers in brackets were subsequently provided by Estonia. 

Table 5.3 

Number of groundwater monitoring sites in Estonia and their purpose  

Monitoring Purpose 

Europea
n Union 
RBD 
Code 

Total 
ground-
water 
monitor-
ing sites 

CHE – 
Chemi-
cal 
status 

DRI - 
Groundwater 
abstraction 
site for 
human 
consumption 

NID - Nutrient 
sensitive area 
under the 
Nitrates 
Directive - 
WFD Annex 
IV.1.iv 

OPE – 
Opera-
tional 
monito
ring 

QUA – 
Quanti-
tative 
status 

SOE - 
EIONE
T State 
of 
Environ
-ment 
monitor
-ing 

SUR - 
Surveill
ance 
monito
r-ing 

EE1 

EE2 

EE3 

238 

312 

4 

0 (144) 

0 (163) 

0 (4) 

0 (65) 

0 (66) 

0 (4) 

0 (48) 

0 (75) 

0 

62 

98 

0 

0 (94) 

0 (98) 

0 (149) 

0 (117) 

0 

0 (4) 

176 

214 

4 

Source: WISE electronic reporting. The numbers in brackets were subsequently provided by Estonia. 

82 

 
 
 
 
5.1.2. Assessment and classification of quantitative status for groundwater 

Map  5.1  displays  the  most  recently  assessed  quantitative  status  of  groundwater  bodies.  It 
shows that 38 out of 39 groundwater bodies (97 %) were in good quantitative status and one (3 

%) was failing good status (Figure 5.1). In terms of area this means that 1 % was failing good 
quantitative status. 

Figure 5.2 shows that, with the exception of three groundwater bodies (high confidence), there 
is low confidence in status classification. All groundwater bodies had and still have a known 

status, in the first and in the second RBMP.  

The  total  number  of  groundwater  bodies  failing  good  quantitative  status  remains  the  same 
since  the  first  RBMP:  one  groundwater  body  and  1  %  in  terms  of  area.  Nevertheless,  the 

RBMP and background documents indicate that groundwater bodies have been subdivided and 
new  ones  have  been  formed.  This  is  stated  in  the  RBMP  as  the  reason  why  all  groundwater 

bodies cannot be directly compared with the results of the first RBMP. 

In all three RBDs water balance was assessed by a comparison of annual average groundwater 

abstraction against the ‘available groundwater resource’ for every groundwater body. 

The  reasons  for  the  failure  of  good  quantitative  status  of  groundwater  bodies  are  shown  in 
Figure 5.3. The one groundwater body is failing good status due to  failing the water balance 

test  which  means  that  the  long-term  annual  average  rate  of  groundwater  abstraction  is 
exceeding  the  available  groundwater  resource.  The  expected  date  of  achievement  of  good 

quantitative status is unknown, as shown in Figure 5.4. 

In  all  RBDs  the  criterion  of  ‘available  groundwater  resource’  has  been  fully  applied  in 
accordance with WFD Article 2(27), and all environmental objectives have been considered in 

status assessment. 

In  total  eight  groundwater  bodies  are  at  risk  of  failing  good  quantitative  status,  all  due  to 
failing the water balance test. 

83 

 
Map 5.1 

Map of the most recently assessed quantitative status of groundwater bodies  

Note: Standard colours based on WFD Annex V, Article 2(2)( 4). 

Source: WISE, Eurostat (country borders) 

84 

GoodPoorUnknownRiver Basin DistrictsCountries outside the EU 
 
  
Figure 5.1  Quantitative  status  of  groundwater  bodies  in  Estonia  for  the  second  RBMP, 

for  the  first  RBMP  and  expected  in  2015.  The  number  in  parenthesis  is  the 
number  of  groundwater  bodies  for  both  cycles.  NB  -  the  period  of  the 

assessment of status for the second RBMP was 2007 to 2012. The year of the 
assessment of status for first RBMP is not known. 

Expected good status in 2015

90% 

Second plan (39)

First plan (26)

97% 

96% 

0%

20%

40%

60%

80%

100%

Good

Poor

Unknown

Not good

Source: WISE electronic reporting 

Figure 5.2  Confidence in the classification of quantitative status of groundwater bodies 

in Estonia based on the most recent assessment of status 

Source: WISE electronic reporting 

85 

 
 
 
Figure 5.3  Reasons for the failure of good quantitative status of groundwater in Estonia 

based on the most recent assessment of status 

Source: WISE electronic reporting 

Notes: 
‘Water balance’ = long-term annual average rate of abstraction exceeds the available groundwater resource which 
may result in a decrease of groundwater levels. 

‘Surface water’ = Failure to achieve Environmental Objectives (Article 4 WFD) for associated surface water 
bodies resulting from anthropogenic water level alteration or change in flow conditions; significant diminution of 
the status of surface waters resulting from anthropogenic water level alteration or change in flow conditions. 

‘Groundwater dependent terrestrial ecosystems’ = Significant damage to groundwater dependent terrestrial 
ecosystems resulting from an anthropogenic water level alteration. 

‘Saline or other intrusion’ = Regional saline or other intrusions resulting from anthropogenically induced 
sustained changes in flow direction. 

86 

 
 
 
Figure  5.4  Expected date of achievement of good quantitative and good chemical status 

of groundwater bodies in Estonia.  

Source: WISE electronic reporting 

5.1.3. Consideration  of  groundwater  associated  surface  waters  and/or  groundwater 

dependent ecosystems 

In 26 out of 39 groundwater bodies there are groundwater associated surface waters and none 
of them are related to a risk. Groundwater associated surface waters have been considered in 

status assessment in all RBDs.  

There are 19 out of 39 groundwater bodies linked to terrestrial ecosystems and none of them 

are linked to an identified risk. Groundwater dependent terrestrial ecosystems and the needs of 
terrestrial ecosystems have been considered in status assessment in all three RBDs. 

5.2.  Main changes in implementation and compliance since the first cycle 

Conclusions with regard to the monitoring of quantitative status of groundwater bodies cannot 
be made due to missing data for the second RBMP.45 

The overall status appears not to have changed. 

The  RBMPs  do  not  contain  separate  chapters  or  summaries  of  changes  or  updates  related  to 

this topic; however some relevant information was found scattered in background documents. 

45  According  to  the  clarifications  provided  by  Estonia,  the  number  of  groundwater  bodies  monitored  for 
quantitative status went from 24 out of a total of 26 groundwater bodies in the 1st RBMPs to 30 out of a total of 39 
groundwater bodies in the second RBMPs. 

87 

 
 
                                                      
The number of groundwater bodies increased by 50 %, from 26 in the first RBMP to 39 in the 

second  RBMP,  but  the  total  groundwater  body  area  remained  almost  the  same.  Four 
groundwater  bodies  remained  unchanged  since  the  first  RBMP,  while  most  groundwater 

bodies have been subdivided and new ones have been created. 

The  RBMPs  mention  that  the  assessment  of  the  improvement  in  the  achievement  of  the 

environmental  objectives  from  the  previous  period  could  not  be  carried  out  unambiguously, 
since  the  boundaries  of  groundwater  bodies  and  the  basics  for  assessing  their  status  have 

changed. For example, the number of groundwater bodies for West-Estonian and East-Estonian 
has  increased  significantly  -  groundwater  bodies  have  been  subdivided  and  new  ones  have 

been created. This is stated in the RBMP as the reason why all groundwater bodies cannot be 
directly compared with the previous RBMP. 

Changes in status assessment have been referred in the RBMP as being due to several reasons 

resulting from the data and methodology used, including: supplementary quality indicators to 
be  determined;  the  results  of  surveys  in  addition  to  monitoring  data;  a  regularly  updated 

monitoring program; and new monitoring wells. It seems that the methodology for determining 
the quantitative status of groundwater bodies might have been updated, but this is not explicitly 

explained in the RBMP. It is therefore not clear whether significant changes took place in the 
assessment methodology. 

Regarding the changes in quantitative status of groundwater bodies, these results are reported 
within certain tables of this topic in all the RBMPs - the change in status is presented using the 

following terms: better,  worse or same (no change happened). For most groundwater bodies, 
quantitative status remained good, the exception being one groundwater body in East-Estonian 

RBD (Ida-Viru oil shale basin groundwater body), for which quantitative status remained poor. 

5.3.  Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first PoM requested action 
on the following: 

  Recommendation: Where there are currently high uncertainties in the characterisation 
of the RBDs, identification of pressures, and in the assessment of status, these need to 

be addressed in the current cycle, to ensure that adequate measures can be put in place 
before  the  next  cycle.  The  methodology  for  identifying  significant  pressures  and 

impacts  is  weak.  The  monitoring  network  was  relatively  weak,  with  a  low  density  of 
monitoring stations. 

88 

 
Assessment: This recommendation concerning uncertainties in status assessment is still 

not  fulfilled  as  confidence  in  status  assessment  remains  generally  low.  The  RBMPs 
indicate  that  the  methodology  for  determining  the  quantitative  status  of  groundwater 

bodies may have been updated, however this is not explicitly explained. 

  Recommendation: There is currently a relatively high proportion of water bodies, both 
groundwater  and  surface  water  bodies  which  are  in  good  or  better  status,  with  the 

exception of the coastal waters that are almost all failing to achieve good status. There 
are also  few  unknowns, despite a monitoring network which was not  WFD compliant 

for the first RBMPs. Estonia needs to confirm this status assessment through the next 
round of surveillance monitoring exercises to ensure confidence in the assessment. 

Assessment: In the WISE reporting on monitoring purposes, Estonia did not report any 
quantitative monitoring in groundwater bodies, while the RBMPs assessed state that all 

groundwater bodies are subject to quantitative monitoring and each RBMP contains a 
whole  sub-chapter  on  this  subject  under  the  chapter  ‘Assessment  of  quantitative 
status’46. The recommendation has been partially fulfilled. 

  Recommendation:  The  review  of  the  assessment  of  groundwater  status  needs  to  be 

completed. 

Assessment:  This  recommendation  cannot  be  assessed  as  in  the  assessed  RBMP  it  is 

indicated that the methodology for determining the quantitative status of groundwater 
bodies might have been updated, but this is not explicitly explained.47 

46 Estonia subsequently clarified that quantitative monitoring was in fact carried out in 30 of the 39 groundwater 
bodies. 
47 Estonia subsequently clarified that the review of the status assessment methodology has now been completed. 

89 

 
 
 
                                                      
Topic  6  Monitoring,  assessment  and  classification  of  chemical 
status of groundwater bodies 

6.1.  Assessment  of 

implementation  and  compliance  with  the  WFD 

requirements in the second cycle 

6.1.1. Monitoring of chemical status in groundwater 

The  total  number  of  groundwater  bodies  is  39.  All  groundwater  bodies  are  subject  to 

surveillance  monitoring  (Table  5.1)  but  not  all  groundwater  bodies  at  risk  are  subject  to 
operational monitoring. In total 11 groundwater bodies (28%) are at risk but in East-Estonian 

nine  groundwater  bodies  are  at  risk  and  only  six  are  monitored  and  in  West-Estonian  two 
groundwater bodies are at risk and five are monitored. 

The number of groundwater bodies increased significantly by 50 % from 26 in the first RBMP 
to 39 in the second RBMP but the total groundwater body area remained almost the same. Four 
groundwater bodies remained unchanged since the first RBMP. 

The number of groundwater bodies with surveillance monitoring increased from 20 out of 26 
in the first RBMP to full coverage (39 groundwater bodies) in the second RBMP. The number 

of monitoring sites is listed in Table 5.3 and shows that the number of surveillance monitoring 
sites has been significantly increased from 154 in the first RBMP to 394 in the second RBMP. 

The  number  of  operational  monitoring  sites  has  been  significantly  increased  since  the  first 
RBMP, from 25 to 160. 

All  substances  at  risk  of  causing  deterioration  in  chemical  status  are  subject  to  surveillance 
monitoring  but  not  all  of  these  substances  are  covered  by  operational  monitoring.  All  WFD 

core parameters nitrate,  ammonium, electrical  conductivity, oxygen  and  pH are monitored in 
all RBDs. 

6.1.2. Assessment and classification of chemical status in groundwater 

Map  6.1  and  Figure  6.1  display  the  most  recently  assessed  chemical  status  of  groundwater 
bodies.  It  shows that 31 out  of 39 groundwater bodies (79 %) were of  good chemical  status, 

and  the  remaining  eight  groundwater  bodies  (21  %)  are  failing  good  status.  In  terms  of  area 
this means that about 5 % are failing good quantitative status. Figure 6.2 shows the confidence 

in status classifications which is medium and mainly low. All groundwater bodies had and still 
have a clear status, in the first and in the second RBMP. 

90 

 
Map 6.1 

Map  of  the  most  recently  assessed  chemical  status  of  groundwater  bodies  in 

Estonia  

Note: Standard colours based on WFD Annex V, Article 2.4.5. 
Source: WISE, Eurostat (country borders) 

91 

GoodPoorUnknownRiver Basin DistrictsCountries outside the EU 
 
 
 
Figure 6.1  Chemical status of groundwater bodies in Estonia for the second RBMP, for 

the  first  plan  and  expected  in  2015.  The  number  in  the  parenthesis  is  the 
number  of  groundwater  bodies  for  both  cycles.  NB  -  the  period  of  the 

assessment of status for the second RBMP was 2007 to 2012. The year of the 
assessment of status for first plan is not known. 

Source: WISE electronic reporting 

Figure 6.2  Confidence  in the classification of chemical status of groundwater bodies in 

Estonia based on the most recent assessment of status 

Source: WISE electronic reporting 

92 

 
 
 
The  total  number  of  groundwater  bodies  failing  good  status  increased  since  the  first  RBMP 

from one (4 %) to eight (21 %) groundwater bodies (Figure 6.1). In terms of groundwater body 
area, the percentage of total groundwater body area at poor status has increased from 1 % in 

the  first  RBMP  to  5  %  in  the  second  RBMP.  The  expected  date  of  achievement  of  good 
chemical status is shown in Figure 5.4. 

The reasons for the failure of good chemical status of groundwater bodies are shown in Figure 
6.3.  For  all  eight  groundwater  bodies  the  general  assessment  of  the  chemical  status  for  the 

groundwater body as a whole failed. This assessment considers the significant environmental 
risk from pollutants across a groundwater body and a significant impairment of the ability to 

support  human  uses.  Figure  6.4  shows  the  pollutants  causing  failure  of  status  and  sustained 
upward trends.  

The calculation of the extent of exceedance of a groundwater quality standard or a groundwater 

threshold  value  is  in  all  RBDs  based  on  the  number  of  monitoring  sites  in  the  groundwater 
body. 

In all RBDs groundwater threshold values have been established for all pollutants or indicators 
of  pollution  causing  a  risk  of  failure  of  good  chemical  status.  The  RBMPs  and  background 
documents  do  not  indicate  that  all  Groundwater  Directive48  Annex  II  substances  have  been 
considered.  In  all  three  RBDs  natural  background  levels  have  been  considered  in  the  status 

assessment.  

A trend methodology is available and assessments have been performed in all RBDs. 

48 Directive 2006/118/EC of the European Parliament and of the Council of 12 December 2006 on the protection 
of 
http://eur-lex.europa.eu/legal-
and 
content/EN/TXT/?uri=CELEX:02006L0118-20140711 

deterioration 

groundwater 

pollution 

against 

93 

 
 
 
 
 
                                                      
Figure 6.3  Reasons  for  failing  good  chemical  status  in  Estonia  for  the  most  recent 

assessment of status 

Source: WISE electronic reporting. 

Notes: 
‘Surface water’ = Failure to achieve Environmental Objectives (Article 4 WFD) in associated surface water 
bodies or significant diminution of the ecological or chemical status of such surface water bodies. 

‘Groundwater dependent terrestrial ecosystems’ = Significant damage to terrestrial ecosystems which depend 
directly on the groundwater body. 

‘Saline or other intrusion’ = Regional saline or other intrusions resulting from anthropogenically induced 
sustained changes in flow direction. 

‘Drinking Water Protected Area’ = Deterioration in quality of waters for human consumption. 

‘General water quality assessment’ = Significant impairment of human uses; significant environmental risk from 
pollutants across the groundwater body. 

6.1.3. Consideration  of  groundwater  associated  surface  waters  and/or  groundwater 

dependent ecosystems 

In 26 out of 39 groundwater bodies there are groundwater associated surface waters and none 
of them are related to a risk. Groundwater associated surface waters have been considered in 

status assessment in all RBDs.  

There are 19 out of 39 groundwater bodies linked to terrestrial ecosystems in each RBDs and 

none of them are linked to identified risks. Groundwater dependent terrestrial ecosystems have 
been considered in status assessment in all RBDs. 

Groundwater associated aquatic ecosystems and groundwater dependent terrestrial ecosystems 
have not been considered in the establishment of groundwater threshold values. 

94 

 
 
 
 
 
Figure 6.4 

Top  ten  groundwater  pollutants  causing  failure  of  good  chemical  status  in 

Estonia 

Source: WISE electronic reporting).  

Note: only 6 pollutants reported causing failure. 

Figure 6.5 

Top ten pollutants with upward trends in groundwater bodies in Estonia 

Source: WISE electronic reporting.  

95 

 
 
 
 
 
 
 
 
 
 
 
Figure 6.6 

Percentage of groundwater bodies in Estonia at risk of failing good chemical 

status and good quantitative status for the second RBMP 

Source: WISE electronic reporting. 

6.2.  Main changes in implementation and compliance since the first cycle 

The  RBMPs  do  not  contain  separate  chapters  or  summaries  of  changes  or  updates  related  to 

this  topic;  however,  some  relevant  information  was  found  in  background  documents,  albeit 
scattered. 

The number of groundwater bodies increased by 50 % from 26 in the first RBMP to 39 in the 

second  RBMP,  in  West-Estonian  and  East-Estonian,  but  the  total  groundwater  body  area 
remained almost the same. Groundwater bodies have been subdivided and new ones have been 

created, only four groundwater bodies remained unchanged since the first RBMP. 

Monitoring of  groundwater bodies has improved. All  groundwater bodies are now subject  to 
surveillance  monitoring  but  not  all  groundwater  bodies  at  risk  are  subject  to  operational 
monitoring.  

The  status  situation  has  deteriorated.  The  total  groundwater  body  area  at  poor  status  has 

increased from 1 % in the first RBMP to 5 % in the second RBMP and from one groundwater 
body  to  eight  groundwater  bodies.  Due  to  the  significant  changes  in  the  delineation  of 

groundwater  bodies,  the  groundwater  bodies  cannot  be  directly  compared.  The  changes  in 
status  results  from  several  factors:  re-delineation/splitting  of  groundwater  bodies;  significant 

change  of  pressures;  a  regularly  updated  monitoring  program;  new  monitoring  wells;  more 

96 

 
 
 
data; the determination  of supplementary quality indicators, and;  a modification of the status 

classification  methodology.  Detailed  explanations  were  not  found  in  the  RBMP.  Also  the 
acceptable extent of exceedances of quality standards and threshold values has been tightened 

(now 20 %). 

The  main  reason  for  the  increasing  number  of  groundwater  bodies  failing  good  status  is 

reported  to  be  the  increasing  exceedances  of  threshold  values,  in  particular  for  phenols, 
nitrates,  pesticides,  petroleum  products  and  PAHs,  by  point  sources  and  diffuse  sources  of 

pollution. 

Although not all groundwater bodies can be directly compared with the first cycle, the updates 
and amendments  contributed to  a more precise  assessment of the status  of each  groundwater 

body. 

6.3.  Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first PoM requested action 
on the following: 

  Recommendation: Where there are currently high uncertainties in the characterisation 
of the RBDs, identification of pressures, and in the assessment of status, these need to 
be addressed in the current cycle, to ensure that adequate measures can be put in place 

before  the  next  cycle.  The  methodology  for  identifying  significant  pressures  and 
impacts  is  weak.  The  monitoring  network  was  relatively  weak,  with  a  low  density  of 

monitoring stations. 

Assessment:  This  recommendation  concerning  uncertainties  in  status  assessment  has 

not been fulfilled as confidence in status assessment is still low. 

  Recommendation: There is currently a relatively high proportion of water bodies, both 
groundwater  and  surface  water  bodies  which  are  in  good  or  better  status,  with  the 

exception of the coastal waters that are almost all failing to achieve good status. There 
are also  few  unknowns, despite a monitoring  network which was not  WFD compliant 

for the first RBMPs. Estonia needs to confirm this status assessment through the next 
round of surveillance monitoring exercises to ensure confidence in the assessment. 

Assessment: This recommendation has been partially fulfilled. All groundwater bodies 
are subject to surveillance monitoring but not all groundwater bodies at risk of failing 

97 

 
good  status  are  subject  to  operational  monitoring.  The  status  results  are  still  of  low 

confidence. 

  Recommendation:  Further  efforts  are  needed  to  ensure  the  monitoring  networks 
become  WFD  compliant,  such  as  to  establish  a  monitoring  programme  for  coastal 

waters, monitoring of all relevant quality elements both in surveillance and operational 
monitoring. 

Assessment: This recommendation has been partially fulfilled. All groundwater bodies 
are subject to surveillance monitoring and all substances causing risk are covered, but 

not  all  groundwater  bodies  at  risk  of  failing  good  status  are  subject  to  operational 
monitoring and not all substances causing risk are covered. 

  Recommendation:  The  review  of  the  assessment  of  groundwater  status  needs  to  be 

completed. 

Assessment:  The  recommendation  cannot  be  fully  assessed  as  in  the  RBMPs  it  is 

indicated that the methodology for determining the quantitative status of groundwater 
bodies  was  updated,  however  it  is  not  explicitly  explained  in  detail  in  the  RBMP  for 
chemical status. 

98 

 
 
 
Topic  7  Designation  of  Heavily  Modified  and  Artificial  Water 
Bodies and definition of Good Ecological Potential 

7.1.  Assessment  of 

implementation  and  compliance  with  the  WFD 

requirements in the second cycle for designation  

7.1.1. Designation of Heavily Modified and Artificial Water Bodies 

Heavily modified water bodies are designated in the categories of rivers and coastal waters and 

artificial water bodies are designated in the categories of lakes and rivers (Figure 7.1). Only a 
few  (5)  river  heavily  modified  water  bodies  are  reservoirs.  These  water  bodies  were  all 

originally rivers. 

The  majority  of  river  heavily  modified  water  bodies  are  designated  due  to  agricultural  land 

drainage.  It  is  outlined  in  the  RBMPs  that  heavily  modified  water  bodies  are  those  water 
bodies  that  are  regularly  dredged  and  redesigned  for  land  improvement  purposes.  The  water 
use  for  which  coastal  water  bodies  are  designated  as  heavily  modified  is  not  specified 
according  to  the  uses  listed  in  WISE  (reported  as  “other”).  The  main  physical  alterations  of 

river  heavily  modified  water  bodies  are  land  drainage  and  weirs/dams/reservoirs.  Coastal 
heavily modified water bodies are affected by weirs/dams/reservoirs. 

A  2008  methodological  background  document,  which  is  applicable  to  the  national  level, 

provides specific information on how significant adverse effects of restoration measures on the 
use  and  the  wider  environment  have  been  defined.  The  methodology  has  established  general 

criteria (not linked to a specific use) for the assessment of significant adverse effects on the use 
and the wider environment (e.g. related to the reduction of the electricity production), effects 

on  employment  and  entrepreneurship,  reduction  of  cultural  history  attractiveness  and  loss  of 
revenue from a tourist attraction. 

The  same  methodology  also  provides  information  on  the  assessment  of  better  environmental 
options  (“other  means”).  Regarding  heavily  modified  water  bodies  designated  due  to  land 

drainage,  it  is  stated  that  the  only  alternative  is  the  construction  of  polder  systems  for  the 
maintenance  of  drained  land.  It  is  concluded  that  this  alternative  is  unpractical  and 

economically expensive. 

99 

 
Figure 7.1 

Proportion  of  total  water  bodies  in  each  category  in  Estonia  that  has  been 

designated as heavily modified or artificial  

Source: WISE electronic reporting  

7.1.2. Definition of Good Ecological  Potential for Heavily Modified  and Artificial  Water 

Bodies 

Good  ecological  potential  is  reported  as  defined  in  all  three  RBDs,  following  the  Common 
Implementation Strategy Guidance approach (approach based on biological quality elements as 

illustrated in Common Implementation Strategy Guidance No 4). Good ecological potential is 
defined  for  groups  of  heavily  modified  water  bodies/artificial  water  bodies  of  the  same 

use/physical modification in all three RBDs. 

A method for good ecological potential has been developed at a national level, which is based 
on the same classification approach as the one used for the ecological status of natural water 
bodies on the basis of monitoring results.  

Good  ecological  potential  is  also  reported  as  defined  in  terms  of  biology  in  the  three  RBDs. 

The  biological  quality  element  for  which  biological  values  have  been  derived  to  define 
maximum and good ecological potential are phytobenthos, macrophytes, benthic invertebrates, 

fish, phytoplankton, macroalgae, and angiosperms. 

However,  according  to  the  information  found  in  the  second  RBMPs,  the  ecological  potential 
seems  to  be  defined  mostly  in  terms  of  hydromorphology.  Biological  values  have  only  been 

derived  in  cases  where  monitoring  data  (survey  monitoring,  operational  monitoring  or  data 

100 

 
 
 
collected through different projects) are available (using methods for status assessments). For 

many  heavily  modified  water  bodies/artificial  water  bodies,  biological  values  have  not  been 
derived,  because  monitoring  data  is  not  available  and  hydromorphology  has  been  used  as  a 

proxy.  

For  rivers,  methods  for  assessing  fish  and  benthic  invertebrates  are  reported  as  sensitive  to 

altered habitats due to morphological changes. For coastal waters, only methods for assessing 
benthic invertebrates are reported as sensitive to hydromorphology. 

Mitigation  measures  for  defining  good  ecological  potential  have  been  reported  in  all  three 

RBDs.  They  are  related  to  continuity  issues  (fish  ladders,  bypass  channels)  and  removal  of 
structures. However, no  description of the  ecological  changes expected due to  the mitigation 

measures was found. 

A comparison between good ecological potential and good ecological status has been made in 
all three RBDs. 

7.2.  Main changes in implementation and compliance since the first cycle 

No significant changes have been noted in the numbers of designated heavily modified water 

bodies and artificial water bodies since the first RBMPs. It is mentioned though that there has 
been an update of the list of heavily modified water bodies based on a report of the Ministry of 

Environment  2014  ("Overview  of  Major  Water  Management  Problems"),  during  which  the 
validity  of  heavily  modified  water  bodies  was  checked,  taking  into  account  updated  status 

assessments. Based on the information found in the second RBMPs, it is concluded that overall 
no  changes  have  been  made  to  the  heavily  modified  water  bodies  designation  methodology 

since the first cycle. 

A  key  change,  however,  concerns  the  definition  of  good  ecological  potential.  In  the  first 

RBMPs,  good  ecological  potential  was  not  defined,  while  in  the  second  RBMPs,  good 
ecological potential is reported as defined for all three RBDs. 

7.3.  Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first PoM requested action 
on the following: 

  Recommendation: The designation of HMWBs should comply with all the requirements 
of  Article  4(3).  The  assessment  of  significant  adverse  effects  on  their  use  or  the 

101 

 
environment and the lack of significantly   better   environmental   options   should   be   

specifically   mentioned   in   the RBMPs. This is needed to ensure transparency of the 
designation process. 

Recommendation: Assess for the second  RBMPs  all  potential  HMWB  in  relation to 
"other means" that can be  a  better  environmental  option  and  restoration  option.  In 

accordance with WFD requirements, take action to restore HMWB if feasible. 

Recommendation:  Be    transparent    for    the    second    RBMP    in    the    HMWB  

designation    process    and    provide    rationale  for  the  changes  done  since  the  first 
RBMP. 

Assessment:  Overall,  the  methodology  for  heavily  modified  water  bodies  designation 

has  not  changed  since  the  first  RBMPs.  The  methodological  document  from  2008 
included  information  on  criteria  for  assessing  substantial  changes  in  character,  and 

general criteria for the assessment of significant adverse effects of measures on the use 
and  wider  environment.  The  methodology  also  provides  general  information  on  the 

assessment of better environmental options (“other means”). 

Information  has  not  been  found  on  the  outcomes  of  the  assessment  of  significant 

adverse effects on the use and of better environmental options for all individual heavily 
modified water bodies. 

Therefore, the recommendation is considered as partially fulfilled. 

102 

 
 
 
 
Topic 8 Environmental objectives and exemptions 

8.1.  Assessment  of 

implementation  and 

compliance  with  WFD 

requirements in second cycle 

8.1.1.  Environmental objectives 

The  environmental  objectives  are  defined  in  Article  4  of  the  WFD.  The  aim  is  long-term 
sustainable water management based on a high level of protection of the aquatic environment. 

Article 4(1) defines the WFD general objective to be achieved in all surface and groundwater 
bodies,  i.e.  good  status  by  2015.  Within  that  general  objective,  specific  environmental 

objectives are defined for heavily modified water bodies (good ecological potential and good 
chemical status by 201549), groundwaters (good chemical and quantitative status by 2015) and 
for Protected Areas (achievement of the objectives of the associated Directives by 2015 unless 
otherwise specified).  

Environmental objectives for ecological and chemical status in surface water and chemical and 
quantitative status in groundwater have been reported in all RBDs. However, for groundwater 

there is a significant number of water bodies where the achievement of status by 2021 or 2027 
is unknown, especially for quantitative status in the Koiva RBD and for chemical status in the 

East-Estonian  RBD.  According  to  the  East-Estonian  RBMP  there  is  also  the  risk  that  some 
groundwater  bodies  might  not  reach  the  environmental  objective  by  2021  due  to  the 

continuation  of  the  extraction  of  oil  shale,  poor  chemical  status  and  increased  inputs  of 
pollutants.  

Member States are also required to specify additional environmental objectives and standards 

in  Protected  Areas  where  these  are  required  to  ensure  the  requirements  of  the  associated 
Directive  are  met.  An  assessment  of  such  additional  objectives  for  Estonia  is  provided  in 

Chapter 15 of this report. 

Assessments  of the current  status  of surface  and groundwater bodies in  Estonia are provided 
elsewhere in this report: for ecological status/potential of surface waters (Chapter 3); chemical 
status  of  surface  waters  (Chapter  4);  quantitative  status  of  groundwater  bodies  (Chapter  5); 

chemical status of groundwater bodies (Chapter 6); status of surface and groundwater bodies 
associated with Protected Areas (Chapter 15). 

49 For priority substances newly introduced by Directive 2013/39/EU, good status should be reached by 2027, and 
for  the  2008  priority  substances,  for  which  the  Environmental  Quality  Standards  were  revised  by  Directive 

2013/39/EU, good status should be reached in 2021. 

103 

 
                                                      
For the second cycle, Member States agreed to report the date when they expect each surface 

and groundwater body to meet its environmental objective. This information is summarised for 
Estonia elsewhere in this report: for ecological status/potential of surface waters (Chapter 3); 

chemical  status  of  surface  waters  (Chapter  4);  quantitative  status  of  groundwater  bodies 
(Chapter 5); chemical status of groundwater bodies (Chapter 6).  

8.1.2.  Exemptions 

Where  environmental  objectives  are  not  yet  achieved  exemptions  can  be  applied  in  case  the 

respective  conditions  are  met  and  the  required  justifications  are  explained  in  the  RBMP. 
Figure 8.1 summarises the percentage of water bodies expected to be at least in good status in 

2015 and the use of at least one exemption for the four main sets of environmental objectives. 

Figure 8.1  Water bodies in Estonia expected to be in at least good status in 2015 and use 
of exemptions. 1 = Surface water body ecological status/potential; 2 = surface 

water  body  chemical  status;  3  =  Groundwater  body  quantitative  status;  4  = 
Groundwater body chemical status 

Source: WISE electronic reporting  For some water bodies the date for achievement of good status is unknown. 

Article  4  of  the  WFD  allows  under  certain  conditions  for  different  exemptions  to  the 

objectives:  extension  of  deadlines  beyond  2015,  less  stringent  objectives,  a  temporary 
deterioration,  or  deterioration  for  /  non-achievement  of  good  status  /  potential  due  to  new 

modifications, provided a set of conditions are fulfilled. The exemptions under WFD Article 4 

104 

 
 
 
include  the  provisions  in  Article  4(4)  -extension  of  deadline,  Article  4(5)  -  lower  objectives, 

Article 4(6) - temporary deterioration and Article 4(7)  - new modifications / new sustainable 
human  development  activities.  Article  4(4)  exemptions  may  be  justified  by:  disproportionate 

cost,  technical  feasibility  or  natural  conditions,  and  Article  4(5)  by  disproportionate  cost  or 
technical  feasibility.  In addition,  Article 6(3) of the Groundwater Directive50  allows Member 
States to exempt inputs of pollutants to groundwaters under certain specified circumstances. 

Figure 8.2 summarises the percentage of water bodies subject to each type of exemption (and 

reason) in relation to the four types of environmental objective in Estonia. 

50 Directive 2006/118/EC of the European Parliament and of the Council of 12 December 2006 on the protection 
of 
http://eur-lex.europa.eu/legal-
and 
content/EN/TXT/?uri=CELEX:02006L0118-20140711  

deterioration 

groundwater 

pollution 

against 

105 

 
                                                      
Figure 8.2 

Type of exemptions applied to surface water and groundwater bodies for the 

second  RBMP 
in  Estonia.  Note:  Ecological  status  and  groundwater 
quantitative status exemptions are reported at the water body level. Chemical 

exemptions  for  groundwater  are  reported  at  the  level  of  each  pollutant 
causing  failure  of  good  chemical  status,  and  for  surface  waters  for  each 

Priority Substance that is causing failure of good chemical status 

Source: WISE electronic reporting 

Application of Article 4(4) 

As in the first cycle Estonia is applying Article 4(4) in the second cycle. In West-Estonian and 

East-Estonian RBDs it seems that the number of applications of Article 4(4) has increased for 
surface waters. While in the first cycle Article 4(4) was not applied in the Koiva RBD it has 

been applied now.  

As  in  the  first  RBMPs,  the  justification  for  surface  water  in  relation  to  Article  4(4)  refers  to 

technical feasibility, disproportional costs and natural conditions. According to the PoM of the 

106 

 
 
second  RBMPs,  exemptions  are  mainly  applied  due  to  technical  feasibility  reasons.  The 

justification outlines that it takes longer to fix the problem than there is time available, or that 
there is no information on the cause of the problem, so the solution cannot be identified. The 

justification  is  supported  by  practical  cases  with  further  details  presented.  A  further 
explanation states that research studies are required first in order to implement measures that 

ensure  to  improve  the  status  of  a  body  of  water.  For  example:  a  significant  number  of 
exemptions  in  the  West-Estonian  and  East-Estonian  RBDs  relate  to  migration  barriers.  For 

some water bodies there are actions intended to improve the fish migration conditions, but due 
to  the  need  for  preparatory  projects  there  is  no  certainty  which  technical  solutions  will  be 

available.  Therefore,  it  is  reported  that  subsequent  improvements  towards  the  objectives  will 
only to be possible if suitable measures are found during the second RBMP cycle.  

According  to  WISE  reporting  the  reasons  for  disproportionate  costs  are  affordability  and 
distribution  of  costs.  The  RBMP  further  refers  also  to  alternative  financing  options  and  the 

assessment  of  affordability  and  solvency  which  led  to  disproportionately  high  costs.  In  the 
assessment the total costs of the measures and the applicable grant schemes were compared. It 

is  stated  that  the  assessment  results  revealed  there  are  no  measure  in  the  PoM  of  the  second 
RBMPs  which  implementation  would  be  unfeasible  due  to  disproportionate  costs.  This 

conclusion  is  expressed  in  the  PoM  Annex  1  (PoM  table  for  surface  water)  where  no  new 
exemptions are linked with Article 4(4). Thus, no additional exemptions have been applied in 

the second RBMP compared to the first RBMP.  

The plan refers to further steps for justifying disproportional costs which include particularly 
studies, assessments and pre-projects agreed upon within the framework of PoM, which aim to 

determine the cost of the measures. According to the PoM there are studies being carried out in 
the  second  cycle  during  which  the  costs  of  measures  will  be  determined,  followed  by 

assessments of affordability and cost-benefit. If needed, the necessary grant schemes must be 
developed  where  a  solvency  analysis  shows  that  the  costs  of  implementing  the  measure  are 
disproportionate. 

According  to  the  PoM  of  the  second  RBMPs,  the  justification  of  natural  reasons  for 
exemptions  relates  primarily to the inertia of ecosystems.  The plan refers to  the fact  that  the 

recovery of several ecosystems takes longer than one WFD cycle after the elimination of the 
pressure (e.g. higher levels of mercury in the Estonian coastal marine fish). Therefore, the PoM 

of the second RBMPs provides time extensions in achieving objectives for coastal water bodies 
as well as for certain lakes and rivers.  

The  drivers  behind  Article  4(4)  exemptions  are  agriculture,  hydropower,  fisheries  and 
aquaculture, forestry and urban development. In addition, the West-Estonian and East-Estonian 

107 

 
RBDs  report  industry  and  transport.  East-Estonian  also  mentioned  as  a  driver  tourism  and 

recreation.  The  drivers  behind  Article  4(4)  in  the  East-Estonian  RBD  for  groundwater  are 
industry and energy.  

The main pressures to surface waters for not meeting good ecological status in all RBDs are 
point and diffuse sources and a variety of hydromorphological alterations. A similar range of 

significant pressures are responsible for exemptions under Article 4(4) in relation to chemical 
status (Table 8.1).  

Table 8.1 

Pressure  responsible  for  Priority  Substances  in  Estonia  failing  to  achieve 
good chemical status and for which exemptions have been applied 

Significant pressure on surface water 
bodies 

1.1 - Point - Urban waste water 

1.3 - Point - IED plants 

1.4 - Point - Non IED plants 

2.1 - Diffuse - Urban run-off 

2.10 - Diffuse ––Other 

2.5 - Diffuse - Contaminated sites or 
abandoned industrial sites 

2.6 - Diffuse - Discharges not connected 
to sewerage network 

4.2.1 - Dams, barriers and locks - 
Hydropower 

4.2.8 - Dams, barriers and locks - Other 

8 - Anthropogenic pressure - Unknown 

Failing 
Priority 
Substances 

Article 4(4) - 
Technical 
feasibility 
exemptions 

Number 

Number 

Article 4(4) - 
Disproportionate 
cost exemptions 

Article 4(4) - 
Natural conditions 
exemptions 

3 

2 

1 

2 

1 

3 

1 

1 

1 

1 

9 

2 

1 

2 

12 

3 

12 

1 

1 

12 

Source: WISE electronic reporting 

2 

2 

1 

2 

3 

1 

1 

7 

12 

12 

12 

The impacts in surface waters are nutrient pollution and altered habitats due to morphological 
changes (includes connectivity) in all basins and chemical pollution in the West-Estonian and 

East-Estonian RBDs. The impacts of Article 4(4) exemptions to groundwater are unknown in 
the  West-Estonian  and  Koiva  RBDs.  In  East-Estonian  RBD  the  impacts  on  groundwater  are 

diminution  of  quality  of  associated  surface  waters  for  chemical  /  quantitative  reasons: 
abstraction  exceeds  available  groundwater  resource  (lowering  water  table),  damage  to 

groundwater-dependent terrestrial ecosystems for chemical / quantitative reasons, and chemical 
pollution. 

108 

 
 
 
 
 
 
 
 
 
 
 
 
Application of Article 4(5) 

Article  4(5)  was  not  used  in  the  first  RBMPs  but  is  newly  applied  in  the  second  cycle  in 
surface waters within the East-Estonian RBD. No Article 4(5) is applied to groundwater. The 

justification is related to disproportionate costs.  

Regarding  justifications  for  applying  exemptions  under  Article  4(5)  it  can  be  seen  from  the 

PoM  that  disproportionate  costs  are  used  as  an  argument  in  the  East-Estonian  RBD  for  one 
water body (Narva reservoir). The general justification given is that it would be unreasonably 

expensive  and  achieving  the  objectives  in  other  ways  is  too  costly.  No  further  explanations 
were provided, including details on the alternative measures. 

The  drivers  behind  the  Article  4(5)  exemption  in  surface  waters  are  industry  and  urban 

development. The impacts of Article 4(5) exemptions are chemical pollution, altered habitats 
and nutrient pollution. 

Application of Article 4(6) 

No exemptions according to Article 4(6) have been applied. 

Application of Article 4(7) 

No exemptions according to Article 4(7) have been applied. However, it remains unclear from 
the RBMPs if the impact of the new modifications on the water status been assessed or if there 

are no new modifications.  

Application of Article 6(3) Groundwater Directive 

No exemptions according to Article 6(3) of the Groundwater Directive51  have been applied in 
either the West-Estonian or Koiva RBDs. According to WISE in East-Estonian the exemption 
has  been  applied  in  two  groundwater  bodies  because  of  disproportionate  costs  and  in  four 

water bodies because of measures that would increase risks. It remains unclear why for these 
water bodies no exemption related to either Article 4(4) or Article 4(5) has been reported in the 

plan. Some information was found in the RBMP and background documents, but only indirect 
links  can  be  made  as  there  is  no  reference  made  to  WFD  Article  4(4),  Article  4(5)  or  the 
Groundwater Directive Article 6(3) regarding exemptions for groundwater bodies. 

51 Directive 2006/118/EC of the European Parliament and of the Council of 12 December 2006 on the protection 
of 
http://eur-lex.europa.eu/legal-
and 
content/EN/TXT/?uri=CELEX:02006L0118-20140711  

deterioration 

groundwater 

pollution 

against 

109 

 
                                                      
For  groundwater  in  East-Estonian  contaminated  sites,  waste  disposal  sites  mining  and 

discharges from not connected sewage systems are reported as the main pressures. 

It  remains  unclear  for  the  East-Estonian  RBD  whether  an  inventory  of  exemptions  from 

measures  required  to  prevent  or  limit  inputs  of  pollutants  into  groundwater  has  been 
established or not.  

As a result, based on the information provided in the East-Estonian RBMP it can be concluded 

that  both  the  WFD  and  the  Groundwater  Directive  exemptions  are  not  properly  applied. 
Moreover,  the  status  may  further  deteriorate  as  no  concrete  or  long-term  measures  are 

established or implemented within the RBMP framework. 

8.2.  Main changes in implementation and compliance since first cycle 

Article  4(5)  was  not  used  in  the  first  RBMPs  but  is  newly  applied  in  the  second  cycle  in 
surface  waters  within  the  East-Estonian  RBD.  Article  4(4)  was  not  previously  applied  in  the 

Koiva RBD but has now been applied. In the West-Estonian and East-Estonian RBDs it seems 
that the number of applications of Article 4(4) has increased. The Member State report for the 

first cycle stated that Article 4(7) was formally not applied in Estonia. However, Estonia had 
reported  six  uses  of  article  4(7)  to  WISE  (four  in  West-Estonian RBD,  two  in  East-Estonian 

RBD) due to "sustainable human development", but limited or no supporting information was 
provided  in  the  first  RBMPs.  Estonia  subsequently  clarified  that  derogations  according  to 

Article 4(7) were given during the preparation of projects, which were expected to bring new 
and  relevant  modifications  for  these  water  bodies.  Later,  this  did  not  seem  to  be  the  case 

anymore and this information was reviewed. In the second RBMPs, no application of Article 
4(7) has been reported. 

8.3.  Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first PoM requested action 
on the following: 

  Recommendation:  The  use  of  exemptions  under  Article  4(7)  should  be  based  on  a 
thorough  assessment  of  all  the  steps  as  requested  by  the  WFD,  in  particular  an 
assessment  on  whether  the  project  is  of  overriding  public  interest  and  whether  the 
benefits  to  society  outweigh  the  environmental  degradation,  and  the  absence  of 

alternatives that would be a better environmental option. Furthermore, these projects 
may only be carried out when all possible measures are taken to mitigate the adverse 

110 

 
impact  on the status of the water. All  conditions for  the application of  Article 4(7) in 

individual  projects  must  be  included  and  justified  in  the  RBMPs  as  earlier  in  the 
project planning as possible. 

Assessment:  There  is  too  little  information  available  to  establish  whether  or  not  this 
recommendation has been fulfilled. No exemptions according to Article 4(7) have been 

applied in the second cycle. However, it remains unclear from the plans if the impact of 
the  new  modifications  on  the  water  status  been  assessed  or  if  there  are  no  new 

modifications.  

  Recommendation:  Improve  transparency  in  the  application  of  exemptions  for  the 
second RBMPs; include the cost effectiveness of measures in the RBMP; and define the 
criteria  for  the  application  of  "technical  unfeasibility",  "disproportionate  costs"  and 

"natural conditions". 

Assessment: The recommendation is partly fulfilled as exemptions are outlined for each 

water body. Based on the information  provided in the East-Estonian RBMP it can be 
concluded  that  neither  the  WFD  nor  the  Groundwater  Directive  exemptions  are 

properly applied although not all groundwater bodies are in good status in 2015. Also, 
there  is  still  a  lack  of  clear  criteria  that  have  been  developed  for  the  application  of 

"technical feasibility", "disproportionate costs" and "natural conditions". 

111 

 
 
 
Topic 9 Programme of measures  

The aim of this chapter is to provide an overview of the PoM reported by Member States; more 

specific  information  on  measures  relating  to  specific  pressures  (for  example  arising  from 
agriculture) is provided in subsequent chapters. 

The  Key  types  of  measures  (KTM)  referred  to  in  this  section  are  groups  of 

measures identified by Member States in the Programme of Measures, which 
target the same pressure or purpose. The individual measures included in the 

Programme  of  Measures  (being  part  of  the  RBMP)  are  grouped  into  Key 
types of measures for the purpose of reporting. The same individual measure 

can be part of more than one Key Types of Measure because it may be multi-
purpose,  but  also  because  the  Key  types  of  measures  are  not  completely 
independent  silos.  Key  types  of  measures  have  been  introduced  to  simplify 

the  reporting  of  measures  and  to  reduce  the  very  large  number  of 
Supplementary Measures reported by some Member States (WFD Reporting 

Guidance 2016).  

A Key Types of Measure may be one national measure but it would typically 
comprise  more  than  one  national  measure.  The  25  predefined  Key  types  of 

measures are listed in the WFD Reporting Guidance 2016. 

The  Key  types  of  measures  should  be  fully  implemented  and  made 
operational within the RBMP planning period to address specific pressures or 

chemical substances and achieve the environmental objectives. 

9.1.  Assessment  of 

implementation  and 

compliance  with  WFD 

requirements in second cycle 

9.1.1.  General issues 

An  indication  as  to  whether  or  not  measures  have  been  fully  implemented  and  made 
operational is when they have been reported as being planned to tackle significant pressures (at 

the  Key  Types  of  Measure  level).  Significant  pressures  are  also  reported  at  the  water  body 
level.  It  would  therefore  be  expected  that  there  would  be  measures  planned  in  the  RBMP  to 

tackle  all  significant  pressures.  For  surface  water,  KTMs  were  reported  for  all  significant 
pressure types, reported  to  be causing  water bodies to  fail to achieve  good status  in  all three 

112 

 
 
 
RBDs.  For  the  West-Estonian  and  East-Estonian  RBDs  KTMs  for  individual  or  groups  of 

substances were also included.  

For groundwater, KTMs were reported for all significant pressure types causing water bodies 

to  fail  to  achieve  good  status  in  the  West-Estonian  and  East-Estonian  RBDs  (except  diffuse 
mining in the West-Estonian RBD) and KTMs for individual or groups of substances were also 

reported, e.g. monobasic phenols, oil fractions C10-40, and polycyclic aromatic hydrocarbons 
in both RBDs. Estonia has reported that there are no significant pressures on groundwater in 

the Koiva RBD. 

Estonia has mapped the number of national basic and supplementary measures against KTMs 
in all three RBDs. No additional KTMs have been developed by Estonia. Five national basic 

measures have been mapped against only three KTMs, and 52 supplementary measures against 
12  KTMs.  Of  the  52  supplementary  measures,  19  %  were  mapped  against  KTM2  -  Reduce 

nutrient pollution from agriculture and a further 19 % against KTM21 - Measures to prevent or 
control  the  input  of  pollution  from  urban  areas,  transport  and  built  infrastructure.  The  basic 

measures reported fulfil only two of the requirements of Article 11(3). Three measures relate to 
the  implementation  of  the  Urban  Waste  Water  Treatment  Directive  (91/271/EEC),  and  one 

relates  to  the  implementation  of  the  Integrated  Pollution  Prevention  Control  Directive 
(96/61/EC) and the Industrial Emissions Directive (2010/75/EU) fulfilling the requirements of 

Article  11(3)(a).  The  one  other  measure  mapped  to  KTM2  -  Reduce  nutrient  pollution  from 
agriculture  is  reported  to  fulfil  the  requirements  of  Article  11(3)(h):  Measures  to  prevent  or 

control  the  input  of  pollutants  from  diffuse  sources  liable  to  cause  pollution.    Estonia  has 
provided  an  inventory  of  national  basic  measures,  which  includes  supplementary  measures, 

and measures for the Koiva RBD.  

The KTMs reported to be tackling significant pressures have all had national measures mapped 

against them in all three RBDs, apart from KTM13 – Drinking water protection measures (e.g. 
establishment  of  safeguard  zones,  buffer  zones  etc.).  This  KTM  has  been  reported  as  being 

operational  to  address  significant  pressures  in  the  East-Estonian  RBD,  but  no  national 
measures have been mapped against this KTM.  

KTMs  have  been  identified  to  address  all  River  Basin  Specific  Pollutants  and  substances 

causing  a  failure  of  objectives  respectively  in  surface  water  and  groundwater  in  the  West-
Estonian  RBD,  and  for  groundwater  in  the  East-Estonian  RBD.  These  include  C10-40  oil 

fractions,  monobasic  phenols  and  polycyclic  aromatic  hydrocarbons  in  both  RBDs,  and  also 
nitrate, sulphate and pesticides in the East-Estonian RBD. There is no information on measures 
to  address  River  Basin  Specific  Pollutants  in  surface  water  in  the  East-Estonian  and  Koiva 

113 

 
RBDs (Estonia has reported that there is no significant pressure on groundwater in the Koiva 

RBD).  

For groundwater the number of water bodies failing objectives due to substances is provided 

for  the  West-Estonian  and  East-Estonian  RBDs.  There  is  no  information  on  River  Basin 
Specific Pollutants causing failure of objectives in surface water. 

Two Priority Substances (mercury and nickel) have been reported to cause failure of objectives 

in  surface  water  in  the  West-Estonian  RBD  and  three  Priority  Substances  (mercury, 
dichloromethane and pentachlorophenol) have been reported as causing failure in surface water 

in  the  East-Estonian  RBD.  The  number  of  water  bodies  failing  objectives  has  also  been 
reported for both RBDs. Both Priority Substances are covered by KTMs in the West-Estonian 

RBD,  whilst  KTMs  have  been  adopted  to  address  mercury  and  dichloromethane  (but  not 
pentachlorophenol) in the East-Estonian RBD. There is no information for the Koiva RBD. 

Estonia reported a significant amount of information on the progress that was expected to have 
been achieved from the implementation of the first PoM. Indicators of the scale and extent of 

the  pressures  or  chemical  substances  to  be  reduced  by  measures  to  achieve  Environmental 
Objectives, and indicators of the remaining measures that are needed to be made operational to 

achieve Environmental Objectives were provided for a wide range of pressures and substances 
in the West-Estonian and East-Estonian RBDs, and for a more limited range of pressures in the 

Koiva RBD for 2015. The level of ambition for the second PoM is significantly reduced, with 
pressures on only three water bodies being addressed in the West-Estonian RBD and pressures 

in seven water bodies being addressed in the East-Estonian RBD. As no information has been 
reported on the number of water bodies expected to fail to  achieve good status as a result of 

significant pressures it is not possible to determine whether the achievements planned for 2015 
have been achieved, nor whether the measures planned to be achieved by 2021 are sufficient. 

Cost-effectiveness  analysis  is  an  appraisal  technique  that  provides  a  ranking  of  alternative 

measures  on  the  basis  of  their  costs  and  effectiveness,  where  the  most  cost-effective  has  the 
highest ranking. For the first PoM Estonia did not undertake a cost-effectiveness analysis. For 

this PoM a combination of quantitative and qualitative cost-effectiveness analyses was carried 
out in all three RBDs to support the selection of new measures proposed.  

A critical factor in the success of the implementation of the PoM is the availability of funding 
to support the investments required. The costs of measures have been reported by Estonia for 

the  first  cycle  (covering  years  2009-15)  as  a  total  of  all  requirements  under  WFD  Article 
11(3)a-l,  Article  11(4)  and  Article  11(5),  and  as  a  total  for  all  three  RBDs  (i.e.  a  total  for 

114 

 
Estonia)  as  €891.6 m.  For  the  second  cycle  total  investment  required  and  annual  operational 

and  maintenance  costs  are  presented  for  the  years  2016-21  separately  for  Article  11(3)a 
requirements  (measures  required  to  implement  Community  legislation  for  the  protection  of 

water) and Articles 11(3)b-l, Article 11(4) and Article 11(5) (all other measures) for all three 
RBDs.  Depreciation  has  been  included  in  the  calculations.  In  the  West-Estonian  RBD  it  is 

planned that a total investment of €88 m is needed for the implementation of measures required 
by Article 11(3)a with annual operation and maintenance costs of €0.242 m during the period 

2016-2021.  An  investment  of  €192m  is  needed  for  the  implementation  of  other  measures 
(required  by  Article  11(3)b-l,  Article  11(4)  and  Article  11(5))  with  annual  operation  and 

maintenance costs of €7.809 m. In the East-Estonian RBD, a €36.45 m investment is needed to 
implement  the  measures  specified  in  Article  11(3)a  with  annual  operation  and  maintenance 

costs of €0.438 m, and €169 m of investment is needed to implement other measures (required 
by  Article  11(3)b-l,  Article  11(4)  and  Article  11(5))  with  annual  operation  and  maintenance 
costs of €5.929 m. In the Koiva RBD no investment is needed for Article 11(3)a measures but 

€2.6 m is of investment is required to implement other measures (required by Article 11(3)b-l, 
Article 11(4) and Article 11(5)) with annual operation and maintenance costs of €0.175 m. In 

total,  Estonia  a  total  investment  of  €488 m  is  needed  –  this  is  almost  half  the  investment 
required for the implementation of the first PoM.  

European Union investment funding figures are presented for the first and second cycles; for 

2009-15  funding  seems  to  be  shown  as  a  total  for  Estonia  as  €613.2 m.  For  2016-21  the 
West-Estonian RBD is expecting to receive €119.27 m, the East-Estonian RBD €104.34 m and 

the Koiva RBD €1.28 m, a total of €224.89 m, just over a third of the European Union support 
received  for  the  first  PoM.  Estonia  has  reported  that  financing  has  been  secured  for  the 

implementation of the second PoM for all sectors. 

Estonia has reported that joint consultation on the RBMPs and the Marine Strategy carried out 
and  that  preparation  of  the  RBMPs  and  PoM  was  co-ordinated  with  the  Marine  Strategy 
Framework  Directive52  in  the  West-Estonian  and  East-Estonian  RBDs,  but  there  was  no 
assessment of the need for additional measures.  The Koiva RBD is landlocked. National and 
RBD specific measures that are relevant to the Marine Strategy Framework Directive and the 

relevant  basic  measure  types  are  listed  for  all  three  RBDs,  including  the  number  of  basic 
measures (marked 0 for the Koiva RBD). 

52 Directive 2008/56/EC of the European Parliament and of the Council of 17 June 2008 establishing a framework 
for  community  action  in  the  field  of  marine  environmental  policy  (Marine  Strategy  Framework  Directive) 
http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32008L0056 

115 

 
                                                      
The RBMPs and Floods Directive53 Flood Risk Management Plans have been integrated in all 
three RBDs. Joint consultation of RBMPs and Flood Risk Management Plans was carried out, 
the objectives and requirements of the Floods Directive were considered in the second RBMPs 

and  PoM,  drought  management  and  use  of  Natural  Water  Retention  Measures  have  been 
included in the PoM, and financial commitments have been secured for flood protection in all 

three  RBDs.  However,  the  design  of  new  and  existing  structural  measures,  such  as  flood 
defences,  storage  dams  and  tidal  barriers,  has  not  been  adapted  to  take  account  of  the  WFD 

environmental  objectives  in  any  of  the  RBDs,  nor  has  WFD  Article  9(4)  been  applied  to 
impoundment for flood protection. 

9.1.2.  Measures related to other significant pressures 

The  only  other  significant  pressure  that  has  been  identified  is  “Anthropogenic  pressures  – 

unknown”  in  surface  water  in  all  three  RBDs.  Indicators  of  the  scale  and  extent  of  the 
pressures  or  chemical  substances  to  be  reduced  by  measures  to  achieve  Environmental 

Objectives, and indicators of the remaining measures that are needed to be made operational to 
achieve  Environmental  Objectives  were  provided  for  2015  and  2021  (none  for  2027).  The 

pressures  were  all  addressed  with  KTM14  “Research,  improvement  of  knowledge  base 
reducing uncertainty”, and the number of water bodies requiring to be tackled was expected to 

be  reduced  considerably  by  2021.  There  is  no  information  for  other  significant  pressures  on 
groundwater. 

9.1.3.  Mapping of national measures to Key Types of Measure 

It  was  expected  that  Member  States  would  be  able  to  report  their  PoM  by  associating  their 
national measures with predefined Key Types of Measure. Key Types of Measure are expected 

to  deliver  the  bulk  of  the  improvements  through  reduction  in  pressures  required  to  achieve 
WFD Environmental Objectives. A Key Type of Measure may be one national measure but it 

would  typically  comprise  more  than  one  national  measure.  Member  States  are  required  to 
report  on  the  national  measures  associated  with  the  Key  types  of  measures,  and  whether  the 
national  measures  are  basic  (Article  11(3)a  or  Article  11(3)b-l)  or  supplementary  (Article 
11(4)). 

Table 9.1 summarises the number of national measures that have been mapped to the relevant 
Key types of measures in Estonia. Also shown is the number of RBDs for which the KTM has 

been  reported.  Table  9.2  then  summarises  the  type  of  basic  measures  associated  with  the 
national measures mapped against the KTM (information is very limited for Estonia). 

53  Directive  2007/60/EC  on  the  assessment  and  management  of  flood  risks  entered  into  force  on  26  November 
2007 http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32007L0060 

116 

 
                                                      
Table 9.1 

Mapping  of  the  types  of  national  measures  to  Key  Types  of  Measure  in 

Estonia  

Key Type of Measure 

National 
basic 
measures 

National 
supplementary 
measures 

Number of 
RBDs 
where 
reported 

KTM1 - Construction or upgrades of wastewater treatment 
plants 

KTM2 - Reduce nutrient pollution from agriculture 

KTM4 - Remediation of contaminated sites (historical 
pollution including sediments, groundwater, soil) 

KTM5 - Improving longitudinal continuity (e.g. establishing 
fish passes, demolishing old dams) 

KTM6 - Improving hydromorphological conditions of water 
bodies other than longitudinal continuity 

KTM7 - Improvements in flow regime and/or establishment 
of ecological flows 

KTM12 - Advisory services for agriculture 

KTM14 - Research, improvement of knowledge base 
reducing uncertainty 

KTM15 - Measures for the phasing-out of emissions, 
discharges and losses of Priority Hazardous Substances or 
for the reduction of emissions, discharges and losses of 
Priority Substances 

KTM16 - Upgrades or improvements of industrial 
wastewater treatment plants (including farms). 

KTM21 - Measures to prevent or control the input of 
pollution from urban areas, transport and built infrastructure 

KTM22 - Measures to prevent or control the input of 
pollution from forestry 

Total number of Mapped Measures 

3 

1 

1 

5 

Source: Member States reports to WISE 

3 

10 

2 

8 

2 

2 

4 

6 

1 

1 

10 

3 

52 

3 

3 

2 

3 

2 

3 

3 

3 

2 

2 

3 

3 

117 

 
 
 
 
 
 
 
 
 
 
 
 
 
Table 9.2 

Type of basic measure mapped to Key types of measure in Estonia  

Key Type of Measure 

Basic Measure Type 

IPPC IED 

Pollutants diffuse 

Urban Waste Water 

KTM1 - Construction or upgrades of wastewater 
treatment plants 
KTM16 - Upgrades or improvements of industrial 
wastewater treatment plants (including farms). 
KTM2 - Reduce nutrient pollution from 
agriculture 

1 

1 

Source: Member States reports to WISE 

Key 

3 

‘IPPC IED’ = Integrated Pollution Prevention Control Directive (96/61/EC) and the Industrial Emissions Directive 
(2010/75/EU) . 
‘Pollutants diffuse’ = Article 11(3)(h): Measures to prevent or control the input of pollutants from diffuse sources liable to 
cause pollution. 
‘Urban Waste Water’ = Urban Waste Water Treatment Directive (91/271/EEC) 

9.1.4.  Pressures for which gaps to be filled to achieve WFD objectives and the Key types 

of measures planned to achieve objectives 

Member  States  are  required  to  report  the  gaps  that  need  to  be  filled  to  achieve  WFD 

Environmental  Objectives  in  terms  of  all  significant  pressures  on  surface  waters  and 
groundwaters, in  terms  of Priority Substances causing  failure of  good  chemical  status  and in 

terms  of  River  Basin  Specific  Pollutants  causing  failure  of  good  ecological  status/potential. 
Member  States  were  asked  to  report  predefined  indicators  of  the  gaps  to  be  filled  or  other 

indicators where relevant. Values for the gap indicators were required for 2015 and 2021, and 
were optional for 2027. 

The  information  reported  in  WISE  on  the  gaps  to  fulfil  to  achieve  good  ecological  status 

include detailed data on the significant pressures on surface and groundwaters that may cause 
failure on the environmental objectives. For chemical  status,  the Member States reported the 

specific chemical substances causing failure. 

This information is reported at the sub-unit level. Sub-units are smaller geographic areas within 

particular  RBDs  identified  by  Member  States.  Not  all  Member  States  have  defined  and 
reported sub-units. 

Member States were required to report which KTMs are to be made operational to reduce the 

gaps to levels compatible with the achievement of WFD environmental objectives. A number 
of  indicators  were  predefined  for  each  KTM.  Values  of  the  indicators  for  the  second  and 

subsequent  planning  cycles  were  also  to  be  reported  to  give  an  indication  of  the  expected 
progress and achievements: the values for 2027 could be optionally reported. This means that 

118 

 
 
 
 
 
 
 
 
the value of the indicator will be reduced with time as measures are implemented. A value of 

zero is comparable with 100 % good ecological status or potential or good chemical status.  

This  information  was  reported  at  sub-unit  level,  or  at  RBDs  level  if  sub-units  have  not  been 

reported by the Member State. 

9.2.  Main changes in implementation and compliance since first cycle 

The level of implementation of the first cycle of PoM in all three RBDs (West-Estonian, East-

Estonian and Koiva) was reported as “all measures started”, but unexpected planning delays, 
lack  of  finance,  and  a  lack  of  a  mechanism  for  implementing  measures  were  identified  as 

obstacles  to  the  implementation  of  the  PoM  in  all  RBDs.  Pressures  causing  failure  of  WFD 
objectives have been identified, including chemical substances, and measures have been put in 

place  for  most  of  these.  Gap  analyses  have  been  reported  for  2015  and  2021,  with  all  gaps 
expected to be closed by 2021. 

For the first  PoM  cost-effectiveness  analysis was not  used for the selection of measures. For 
the second PoM a combination of quantitative and qualitative cost-effectiveness analyses was 

carried out in all three RBDs to support the selection of new measures proposed. 

New legislation or regulations to implement the PoM in the first cycle was reported necessary 
and already adopted in all three RBDs. 

9.3.  Progress with Commission recommendations 

  Recommendation: Where there are currently high uncertainties in the characterisation 
of the RBDs, identification of pressures, and in the assessment of status, these need to 

be addressed in the current cycle, to ensure that adequate measures can be put in place 
before the next cycle. 

Assessment:  (cid:157)Pressures  causing  failure  of  WFD  objectives  have  been  identified, 
including chemical substances, and measures have been put in place for most of these. 

From  a  Topic  9  perspective  this  recommendation  has  been  fully  addressed.  (Further 
relevant information may be obtained from Chapters 2-6).  

  Recommendation:  Estonia  needs  to  improve  its  information  relating  to  costs  of 
the  calculation  of  disproportionate  costs, 

including  ensuring 

measures, 

that 

distinguishes between costs for basic and supplementary measures. 

119 

 
Assessment:  The  costs  of  measures  have  been  reported.  (Further  information  may  be 

gained from Chapters 8 and 14).  From a Topic 9 perspective this recommendation has 
been fully addressed. 

  Recommendation:  Focus  in  the  second  RBMP  cycle  on  better  linking  pressures  to 
impacts  and  measures,  including  by  source  apportionment,  and  provide  a  clear 
assessment  of  how  many  of  the  pressures  (and  their  sources)  have  to  be  reduced  to 

achieve the WFD goals. 

Assessment: This has been addressed in the gap analyses, with all gaps expected to be 

closed  by  2021.  From  a  Topic  9  perspective  this  recommendation  has  been  fully 
addressed. 

  Recommendation: Integrate the action plan for the Ordovician Ida-Viru oil-shale basin 

in the Programme of Measures of the second RBMPs. 

Assessment:  The  data  reported  to  WISE  do  not  contain  any  reference  to  this,  except 

that  the  River  Basin  Specific  Pollutants  which  are  being  addressed  in  groundwater  in 
the  East-Estonian  RBD  where  Ida-Viru  is  situated  include  C10-40  oil  fractions, 
pollutants that could be related to an oil-shale basin. No reference could be found in the 

RBMPs  and  background  documents  uploaded  to  WISE  to  the  action  plan  for  the 
Ordovician Ida-Viru oil-shale basin in the East-Estonian RBMP, including in the PoM. 

There is also no indication that there are plans in place for the preparation of the action 
plan54.  

  Recommendation: Make more explicit the links between other supporting programmes 
and  legislation  relevant  to  the  WFD,  such  as  urban  wastewater  treatment  and 
programmes for Nitrate Vulnerable Zones (NVZs). The contribution of these supporting 

programmes  to  achieving  the  objectives  of  the  WFD  should  be  shown  in  quantitative 
terms. 

Assessment:  Measures  reported  in  the  second  PoM  include  KTM1  -  Construction  or 
upgrades of urban wastewater treatment plants, and KTM2 - Reduce nutrient pollution 

from  agriculture;  gap  indicators  are  reported  as  “number  of  water  bodies  requiring 
measures”. This recommendation has been partially addressed. 

54  Estonia  subsequently  clarified  that  there  are  measures  for  Ida-Viru  groundwater  bodies  related  with  oil  shale 
mining  in  the  PoM.  In  addition  measures  for  groundwater  protection  are  also  set  in  an  oil  shale  sectoral 
development plan´s action plan. 

120 

 
 
                                                      
Topic 10 Measures related to abstractions and water scarcity  

10.1. Assessment  of 

implementation  and  compliance  with  the  WFD 

requirements in the second cycle 

10.1.1.  Water exploitation and trends  

Water  abstraction  pressures  are  not  reported  as  relevant  for  Estonia,  with  the  East-Estonian 
RBD  having  5  %  of  groundwater  bodies  in  bad  quantitative  status.  The  Water  Exploitation 

Index+ is not calculated, but water quantity data have been reported within Europe’s State of 
Environment  report.  Water  scarcity  is  not  considered  an  issue  at  the  international  level.  The 

RBMPs include a water resource allocation and management plan. 

10.1.2.  Main uses for water consumption  

No data have been reported for the uses of water consumption because water quantity pressures 

are not reported as significant.  

10.1.3.  Measures related to abstractions and water scarcity  

Regarding  basic  measures  (Article  11(3)(e)),  there  is  a  concession,  authorisation  and/or 
permitting  regime  to  control  water  impoundment  and  abstractions  as  well  as  a  register  of 

impoundments and abstractions for surface and groundwater. Small abstractions are exempted 
from  these  controls.  Measures  promoting  efficient  and  sustainable  water  use  (Basic  Measure 

Article  11(3)(c))  were  implemented  in  the  first  cycle,  and  new  measures  and/or  significant 
changes were planned for the second cycle. 

Measures  for  the  prior  authorisation  of  artificial  recharge  or  augmentation  of  groundwater 
bodies (Article 11(3)(f)) were implemented in the first cycle, and new measures or significant 
changes are planned for the second cycle. 

Complementary  measures  under  KTMs  are  reported  for  addressing  abstraction  pressures  on 

groundwater  in  the  East-Estonian  RBD:  KTM13  -  Drinking  water  protection  measures  (e.g. 
establishment  of  safeguard  zones,  buffer  zones  etc.),  KTM14  -  Research,  improvement  of 

knowledge base reducing uncertainty and KTM21 - Measures to prevent or control the input of 
pollution from urban areas, transport and built infrastructure. These all target urban water use. 

The KTM also seem to close the gap until 2021 according to the indicators reported (pressure 
indicators seem to drop to zero in 2021) and no further measures are indicated after 2021. 

Water reuse is not foreseen as a measure. 

121 

 
10.2. Main changes in implementation and compliance since the first cycle 

As stated above, new measures promoting efficient and sustainable water use were planned for 
the second cycle and  changes were also  planned in  the second cycle with  regard to  the prior 

authorisation of artificial recharge or augmentation of groundwater bodies. 

10.3. Progress with Commission recommendations 

There were no Commission recommendations on this topic. 

122 

 
 
 
Topic 11 Measures related to pollution from agriculture  

11.1. Assessment  of 

implementation  and  compliance  with  the  WFD 

requirements in the second cycle 

Agriculture is assessed as a significant pressure on water quality (nutrients) and morphological 

changes due to drainage in all RBDs in surface water and groundwater. Pesticides are an issue 
for groundwater in the East-Estonian RBD. While in the first cycle soil erosion was mentioned 

as  a  significant  pressure,  this  is  not  the  case  in  the  second  cycle.  Measures  implemented  are 
reported to match the pressures. At the time of PoM drafting a specific so-called second phase 

of  the  pressure  analysis  and  risk  assessment  had  been  carried  out.  During  this  additional 
pressure analysis, mapped pressure sources were associated with the status of the water body 

and the quality elements causing the less-than-good status. 11 water bodies were assigned as 
“endangered”. However, it is further stated that only a quantitative characterisation of diffuse 

pressure was made. Therefore, it is unclear from the RBMPs how precisely they have defined 
sources of nitrate and phosphate pollution or if it is done at all.  

In Estonia, measures to reduce leaching from agricultural and arable land are largely integrated 
into  the  Water  Act  (quantitative,  time-based  and  location-based  restrictions  on  fertilizer  and 

manure  spreading)  and  the  Industrial  Emission  Act  (large  farm  complexes).  These  measures 
are also applied outside Nitrate Vulnerable Zones. In the second RBMP period, supervision of 

these requirements is said to be taking place and possibly, it is one of the ways to check if the 
relevant measures  are targeted  at  the right  farmer/right  location in  the second RBMPs. Also, 

measures  for  agricultural  diffuse  pressure  have  a  link  with  the  support  mechanisms  for 
environmentally  sound  management planned in  the Estonian Rural  Development  Plan. There 

are several types of measures taken into consideration to help deliver the WFD, from studies 
and administrative measures to technical measures.  

Technical  measures  are  basic  and  supplementary  measures  under  KTM2  -  Reduce  nutrient 

pollution from agriculture (e.g. Controlling the existence of manure storage facilities and their 
environmental compliance, tightening the threshold for livestock units related to the obligation 

to  maintain  a  manure  storage  facility,  revision  of  the  requirements  set  in  the  integrated 
environmental  permits  issued  for  the  large  farms  and  if  necessary,  setting  stricter 

requirements). The majority of the KTM2 measures are mandatory (14 out of 18).  

No  national  measures  associated  with  KTM3  -  Reduce  pesticides  pollution  from  agriculture 

have been established for Estonian RBMPs. 

123 

 
There  are  five  supplementary  KTM12  measures  established  and  they  all  are  voluntary. 

Hydromorphological measures are also applied. It should be noted that neither the RBMPs nor 
the  Programmes  of  Measures  have  explicitly  associated  the  planned  measures  with  KTM 

codes, including no added information if the measures are assigned as mandatory or voluntary 
or  both.  It  should  be  noted  that  the  background  documents  used  to  provide  the  information 

below have not been published yet:  

Basic measures (Article 11(3)(h)) for the control of diffuse pollution from agriculture at source 

are  applied  only  in  Nitrate  Vulnerable  Zones  except  in  Koiva  where  the  same  rules  apply 
across the whole RBD. General binding rules in line with Article 11(3)(h) of WFD to control 

diffuse pollution are applied in all basins. In the West-Estonian and East-Estonian RBDs, there 
are differentiated rules for different parts of the RBDs. In Estonia the same rules apply across 

the whole RBD, but only for other pollutants (not nitrates and phosphorus). No information is 
provided on the area of agricultural land to be covered by measures to achieve environmental 

objectives. It appears that no gap assessment was performed. 

Since  KTM13  -  Drinking  water  protection  measures  are  targeted  primarily  at  groundwater 
protection  in  Estonia,  the  relevant  information  regarding  these  measures  is  not  found  in  the 

background  document  mentioned  above.  However,  some  associations  with  KTM13  are 
provided  in  the  PoM  in  Annex  2,  which  was  prepared  for  groundwater.  Based  on  Annex  2 

there is one measure related to KTM13 that has been established for some of the groundwater 
bodies (but no details as to whether it is mandatory or voluntary): preparation of projects for 

the groundwater recharge areas that covers drinking water protection areas. It is presented as 
research or a study. 

However, mandatory safeguard zones are established around protection areas that are used or 
intended  to  be  used  for  drinking  water  and  which  have  a  project-specific  daily  water 
abstraction  of  more  than  10m3  or  serving  more  than  50  people.  In  order  to  prevent  the 
deterioration of water quality and to protect the facilities of water protection areas, movement 

is  limited  and  economic  activity  restricted  in  the  area,  except  for  service  of  water  supply 
facilities, forest maintenance, mowing (of grasses), and water monitoring. Another objective is 

to protect the water from diffuse pollution (in particular, nitrogen and phosphorus) for which 
the  relevant  measures  (obligations,  restrictions)  are  mostly  established  in  national  legal  acts. 

These are the measures that have not been separately presented in the RBMPs, for the purpose 
of avoiding duplication with legislation. In the RBMPs assessed, it has been acknowledged that 

diffuse pollution from agriculture, in particular, threatens the quality of shallow groundwater in 
unprotected  groundwater  areas.  It  is  stated  that  the  measures  for  reduction  of  leaching  from 

agricultural lands are largely integrated into the national legal  acts  - Water Act (quantitative, 

124 

 
time-  and  location-based  restrictions  on  fertilizer  and  manure  spreading)  and  the  Industrial 

Emission Act (large livestock farms). In the next RBMP period, a review of these requirements 
is said to be taking place. In very general terms it is indicated that the actions assigned in the 

previous PoM (first cycle) have been implemented, although they are mainly measures which 
are  continuous  (diffuse  pollution)  or  divided  into  phases  (point-source  pollution)  which  will 

continue to be implemented in the next RBMP period (second cycle). 

Based on the RBMPs and Programmes of Measures assessed, additional control measures on 

land  to  prevent  diffuse  pollution  have  been  considered,  however  not  very  explicitly.  It  is 
indicated in the Programmes of Measures that with the help of modelling it will be considered 

whether the diffuse pollution from agriculture is dominant in total nutrient pollution of a water 
body. Forestry and populated areas (10 people/ha or more) without public sewerage are other 

significant diffuse pollution sources An additional criterion of relevance used was the (nature) 
conservation status of a water body, for example, water bodies where the nature conservation 
regulation  calls  for  habitat  restoration  are  prioritised  (considered  to  be  more  relevant).  The 

following  control  measures  to  prevent  diffuse  pollution  (not  necessarily  additional)  that  are 
presented in the Programmes of Measures are: 

  additional supervision over compliance with environmental requirements (measures for 

the protection of surface water and groundwater) in livestock buildings; 

  additional control for misuse of fertilizers (enhanced monitoring); 

  supplementary supervision over farm record keeping; 

 

following  the  time-based  and  quantitative  restrictions  on  the  application  of  fertilizer 
and manure to minimise the nutrient pollution from agricultural land; 

  coordination and approval of layout plans for liquid manure storage; 

Additionally,  it  is  outlined  that  for  water  bodies,  for  which  ecological  status  is  unclear  i.e. 

where  pollution  sources  not  clearly  identified  and/or  where  no  effective  measures  currently 
exist, further studies are needed. 

Based  on  the  information  about  the  measures  provided  in  the  Programmes  of  Measures,  the 

RBMPs  intend  to  rely  mostly  on  mandatory  measures.  There  are  no  significant  differences 
between the RBDs in that regard. 

125 

 
Farmers/Farmers'  Unions  have  been  consulted  under  the  Public  Consultation  process  in  all 

basins.  

In the first cycle financial commitments were not clear; in the second cycle it is reported that 

financing  of  measures  is  secured  in  all  basins.  Information  on  investments  for  agricultural 
measures between 2009 and 2015 is provided.  

11.2. Main changes in implementation and compliance since the first cycle 

In the first cycle, soil erosion was mentioned as a significant pressure but this is stated not to 
be the case in the second cycle. Measures implemented are reported to match the pressures in 

the second cycle. No gap assessment was carried out. 

In  the  next  RBMP  period,  a  review  of  requirements  relating  to  diffuse  pollution  from 

agriculture (in particular, associated with risks to the quality of shallow aquifers in unprotected 
groundwater  areas)  is  said  to  be  taking  place.  In  very  general  terms  it  is  indicated  that  the 

actions  assigned  in  the  previous  PoM  (first  cycle)  have  been  implemented.  Mainly  those  are 
measures  which  (by  the  nature  of  their  implementation)  are  either  continuous  (for  diffuse 

pollution)  or  phased  (for  point-source  pollution)  measures  that  have  continued  to  be 
implemented in the second cycle. 

For  water  bodies  for  which  ecological  status  is  unclear,  pollution  sources  are  not  clearly 
identified  and/or  where  no  effective  measures  currently  exist,  further  studies  have  been  and 

will be implemented. 

In the first cycle, financial commitments were not clear; in the second cycle it is reported that 

financing of measures is secured for all basins. 

11.3. Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first PoM requested action 

on the following: 

  Recommendation: Make more explicit the links between other supporting programmes 
and  legislation  relevant  to  the  WFD,  such  as  urban  wastewater  treatment  and 

programmes for Nitrate Vulnerable Zones (NVZs). The contribution of these supporting 
programmes  to  achieving  the  objectives  of  the  WFD  should  be  shown  in  quantitative 
terms. 

Assessment:  In  all  the  RBMPs  assessed,  there  is  a  separate  chapter  for  other 
programmes  and  plans  that  are  to  be  considered  in  the  process  of  the  RBMP.  The 

126 

 
following supporting programmes are presented: Action Plan for the Nitrate Vulnerable 

Zone  (Nitrate  Vulnerable  Zone),  Baltic  Sea  Action  Plan,  and  the  Estonian  Marine 
Strategy. However, there is a lack of quantitative assessment of their contribution. For 

example, regarding the Nitrate Vulnerable Zone Action Plan, all that is stated is that its 
main  objective  is  to  help  achieve  the  objectives  set  by  the  RBMPs  –  to  achieve  or 

preserve the good status of the water bodies and ensure safe drinking water for people 
by  the  management  of  nitrogen  load  from  agricultural  production.  No  further 

assessment  or  numbers  are  provided  on  how  exactly  this  action  plan  supports  the 
implementation of the RBMPs. Regarding the measures of the Baltic Sea Action Plan; 

the relevant ones are included and integrated in the PoM of the RBMPs, according to 
relevance  in  specific  water  bodies.  These  certain  measures  are  outlined  with  their 

unique  codes  in  this  RBMP  chapter.  But  there  is  no  quantitative  assessment  of  their 
contribution. It is just stated that the objective of the planned measures is ensuring the 
good  status  and  sustainability  of  the  marine  environment  of  the  Baltic  Sea.  As  it  is 

noted  in  the  RBMPs,  the  PoM  only  reflect  the  measures  that  are  directly 
needed/foreseen  for  achieving  the  environmental  objectives  of  the  WFD  -  good 

ecological  status  of  water  bodies.  The  same  conclusion  goes  for  the  Estonian  Marine 
Strategy  –  the  objective  has  been  presented,  but  there  is  no  quantitative  assessment. 

Some  consolation  lies  in  the  fact  that  the  preparation  of  the  Marine  Strategy 
Programme  and  also  the  Baltic  Sea  Action  Plan  was  carried  out  in  parallel  with  the 

drafting of the RBMPs.  

The recommendation has been partially fulfilled. 

  Recommendation:  Estonia  needs  to  further  develop  co-operation  with  farmers  at  the 
different stages of the preparation of the Programme of Measures. This is important, as 
it will ensure technical feasibility, acceptance and the expected success. 

Assessment: Farmers have been consulted and binding requirements to control nutrient 
pollution have been established. The recommendation has been fulfilled. 

  Recommendation:  Put  in  place  measures  in  line  with  Article  11(3)(h)  of  WFD  to 
control  diffuse  pollution  (controls  mean  binding  requirements  -  not  voluntary 

measures, such as the code of good practice). 

Assessment:  General  binding  rules  in  line  with  Article  11(3)(h)  of  WFD  to  control 

diffuse pollution are applied in all basins. In EE1 and EE2 there are differentiated rules 
for  different  parts  of  the  RBDs.  In  EE  the  same  rules  apply  across  the  whole  RBD. 

Only  other  pollutants  are  covered  by  then,  but  not  nitrate  and  phosphorus.  So  this 
recommendation has not been fulfilled.  

127 

 
 
Topic  12  Measures  related  to  pollution  from  sectors  other  than 
agriculture  

12.1.  Assessment  of 

implementation  and 

compliance  with  WFD 

requirements in second cycle 

In  the  context  of  this  topic,  pollution  is  considered  in  terms  of  nutrients,  organic  matter, 
sediment,  saline  discharges  and  chemicals  (Priority  Substances,  River  Basin  Specific 

Pollutants,  groundwater  pollutants  and  other  physico-chemical  parameters)  arising  from  all 
sectors  and  sources  apart  from  agriculture.  Key  types  of  measures  (KTM)  are  groups  of 

measures identified by Member States in their Programmes of Measures which target the same 
pressure or purpose. A KTM could be one national measure but would typically comprise more 

than  one  national  measure.  The  same  individual  measure  can  also  be  part  of  more  than  one 
KTM  because  it  may  be  multipurpose  but  also  because  the  KTMs  are  not  completely 

independent of one another. 

Eight  KTMs,  relevant  to  non-agricultural  sources  of  pressures  causing  failure  of  WFD 

objectives, have been reported for all RBDs in Estonia. These KTMs are: 

  KTM1 – Construction or upgrades of wastewater treatment plants. 

  KTM4 – Remediation of contaminated sites. 

  KTM13 – Drinking water protection measures 

  KTM 14 – Research, improvement of knowledge base reducing uncertainty. 

  KTM15 - Measures for the phasing-out of emissions, discharges and losses of Priority 
Hazardous  Substances  or  for  the  reduction  of  emissions,  discharges  and  losses  of 
Priority Substances. 

  KTM16  -  Upgrades  or  improvements  of  industrial  wastewater  treatment  plants 

(including farms). 

  KTM21  –  Measures  to  prevent  of  control  the  input  of  pollution  from  urban  areas, 

transport and built infrastructure.  

  KTM22 – Measures to prevent or control the input of pollution from forestry. 

128 

 
KTM13 is reported only for the East-Estonian RBD while the other eight KTMs are reported in 

both the East- and West-Estonian RBDs. Three KTMs are reported for the Koiva RBD.  

The  WFD  specifies  that  Programmes  of  Measures  shall  include,  as  a  minimum,  “basic 

measures” and, where necessary to achieve objectives, “supplementary measures” when basic 
measures are not enough to address specific significant pressures. Quantitative information on 

basic  and  supplementary  measures  used  to  tackle  pollution  from  non-agricultural  sources 
(number of measures per KTM) has been provided for most Estonian RBDs. However, for the 

West-Estonian  and  East-Estonian  RBDs  this  information  has  been  provided  for  two  KTMs 
only and no such information has been provided for the Koiva RBD. 

Estonia  provided  more  information  on  basic  measures  required  under  Article  11.3(c  to  k). 

Authorization and/or permitting regimes to control waste water point source discharges  are in 
place  in  all  RBDs  for  surface  and  groundwater.  A  register  of  waste  water  discharges  (Basic 

measures  Article  11(3)(g))  is  available  in  all  Estonian  RBDs  for  surface  and  groundwater. 
Small discharges are exempted from controls in all Estonian RBDs. Some direct discharges to 

groundwater are authorised in accordance with Article 11(3)(j) in all Estonian RBDs. 

At present, the reporting to WISE states that there are measures in place to eliminate or reduce 

pollution from  Priority Substances  and other substances  (Basic measures  Article 11(3)(k)) in 
all  Estonian  RBDs.  In  the  West-Estonian  and  East-Estonian  RBDs,  KTMs  have  been  made 

operational  to  reduce  pressures  from  specific  Priority  Substances  and  River  Basin  Specific 
Pollutants that are causing non-compliance. 

The  Estonian  RBMPs  state  that  the  monitoring  programmes  of  2010-2013  found  the 

concentrations of the majority of Priority Substances identified in the water bodies to be below 
the environmental quality standards; however in the West-Estonian and East-Estonian RBDs, 

exceedances have occurred. In the East-Estonian RBD this was reported to have happened for 
heptachlor  epoxide,  pentachlorophenol,  fluoranthene,  nonylphenols,  octylphenols,  and 

brominated  diphenylethers.  The  main  pressure  sources  of  Priority  Substances  in  the  East-
Estonian  RBD  were  wastewater  treatment  plants,  bottom  sediments  and  oil  shale  extraction 

and treatment activities. The Priority Substances for which exceedances were determined in a 
few  samples  in  the  West-Estonian  RBD  were  di(2-ethylhexyl)phthalate  (DEHP),  nickel, 

nonylphenols and octylphenols. The main pressure sources of Priority Substances in the West-
Estonian  RBD  were  wastewater  treatment  plants,  bottom  sediments,  industrial  areas  and 

diffuse pollution.  

129 

 
Measures have been planned for all those Priority Substances causing status failure, however in 

a very general manner. For example, the RBMPs assessed do not explicitly associate individual 
Priority  Substances  that  cause  failure  with  particular  KTMs  or  other  measures.  Instead,  only 

measures mainly  aimed at  understanding the sources of Priority Substances are applied;  they 
are across all RBDs and are of an administrative nature: 

 

registration of hazardous chemicals in the National Chemical Register; 

 

inventory of hazardous chemicals; 

  clarification and tightening of requirements for Priority Substances in water legislation; 

  additional monitoring of priority hazardous substances in industry; and 

 

informing the population on the management of Priority Substances. 

The  RBMPs  also  mention  the  need  to  continue  exploring  the  possibilities  of  removing 

historical pollution from contaminated sites. 

It is of note that for about 84 % of over 2,400 surface water bodies there is still no information 
on chemical status.  

There is very little information about River Basin Specific Pollutants in Estonia. It is has been 
stated  in  the  RBMPs  that  River  Basin  Specific  Pollutants  in  the  first  RBMPs  were  not 

addressed  because  they  were  not  identified.  For  the  second  cycle  it  is  stated  that  these 
pollutants and their limit values are based on the corresponding substances identified in other 

countries  and  their  limit  values  are  adapted  to  the  local  circumstances,  based  on  expert 
judgment. There have been 31 River Basin Specific Pollutants added to the relevant regulation 

under  the  Estonian  Water  Act.  Based  on  the  PoM  Annex  1  concrete  measures  have  been 
planned for barium and phenols in the West-Estonian and East-Estonian RBDs, and these two 

River Basin  Specific Pollutants appear to  be the  main substances  causing failure. A study of 
potential natural concentrations and potential sources of these two substances is planned at the 

national level. There are also zinc and petroleum products considered as River Basin Specific 
Pollutants  causing  failure,  however  measures  addressing  these  are  more  general,  mostly  of 

administrative nature (usually supervision and updating of the requirements that had been set 
previously). KTMs have been reported for other River Basin Specific Pollutants (As, Ni) but 

no information on these was found in the RBMP. There are no River Basin Specific Pollutants 
causing failure in the Koiva RBD, but this is probably due to gaps in monitoring. 

130 

 
Based on the PoMs Annex 2, it can be concluded that measures are planned for all pollutants 

causing failure of good chemical status in groundwater. Measures are particularly established 
in  the  East-Estonian  RBD  which  contains  most  (seven)  of  the  Estonian  groundwater  bodies 

that  have  failed  to  meet  good  chemical  status.  Most  of  the  measures  planned  for  these 
pollutants  are  of  a  research  type:  pre-assessment  or  pollution  study.  Additional  measures 

include  safe  disposal  of  the  residual  waste,  construction  or  upgrading  of  water  treatment 
systems in landfills, construction of treatment systems for storm water and other contaminated 

water in oil products storage facilities. The pollutants causing failure of good chemical status 
are mainly phenols, toluene, xylene, PAH and petroleum products. 

Wastewater  treatment  related  measures  were  part  of  the  PoM  in  the  first  RBMP,  and  the 
continuation  of  their  implementation  is  planned  also  in  the  second  RBMP.  In  some  cases, 

industrial wastewater is a pressure causing poor status. It is stated in the RBMPs that additional 
measures  should  be  set  within  environmental  permits,  targeting  the  upgrade  of  wastewater 

treatment plants. The monitoring of industrial wastewater discharges must also be improved. It 
is  acknowledged  in  the  RBMPs  that  a  particular  problem  that  needs  to  be  given  a  lot  more 

attention in the second cycle is the control of emissions of hazardous substances. The control 
of the use of hazardous substances should be organised and made more systematic in order to 

avoid their introduction into water bodies. An important issue is the distribution of the roles of 
controlling hazardous substances between the different parties, also the respective obligations 

and  rights  must  be  clarified  so  that  priority  hazardous  substances  can  be  avoided  and  the 
emissions  of  hazardous  substances  reduced.  Measures  aiming  at  limiting  emissions  of 

hazardous substances are of an administrative nature. 

12.2.  Main changes in implementation and compliance since first cycle  

It was mentioned in the first RBMPs concerning substance specific measures that an inventory 
and source tracking of pollution should be carried out in water bodies in which exceedance of 

threshold  values  for  phenols  and  oil  products  had  been  revealed  by  monitoring.  Measures 
implemented in order to reduce discharges of phenols into the water environment are described 
in a national programme. 

12.3.  Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first  PoM requested action 

on the following: 

131 

 
  Recommendation: Estonia needs to complete the identification of sources of chemical 
pollution, to enable effective measures to be put in place to reduce chemical pollution 
for priority substances, and other pollutants, and then progressively reduce and phase-

out priority hazardous substances where relevant.  

Assessment:  Estonia  reported  that  measures  are  planned  or  in  place  to  eliminate  or 

reduce  pollution  from  Priority  Substances  and  other  substances  causing  failure; 
however  they  are  of  a  very  general  nature.  For  example,  the  RBMPs  assessed  do  not 

explicitly associate individual Priority Substances that cause failure to particular KTMs 
or other measures. Instead, only measures mainly aimed at understanding the sources of 

Priority  Substances  are  applied;  they  are  applied  across  all  RBDs  and  are  of  an 
administrative nature. Therefore this recommendation has only been partially fulfilled.  

  Recommendation: Make more explicit the links between other supporting programmes 
and  legislation  relevant  to  the  WFD,  such  as  urban  wastewater  treatment  and 
programmes for Nitrate Vulnerable Zones (Nitrate Vulnerable Zones). The contribution 

of  these  supporting  programmes  to  achieving  the  objectives  of  the  WFD  should  be 
shown in quantitative terms. 

Assessment: Measures to tackle urban point sources are reported in all RBDs and they 
are also quantified in the East Estonian and West Estonian RBDs, but not in the Koiva 

RBD.  

In all the RBMPs assessed there is a separate chapter for other programmes and plans 

that  are  to  be  taken  into  account  in  river  basin  management  planning.  The  following 
supporting  programmes  are  presented:  Action  Plan  for  the  Nitrate  Vulnerable  Zone, 

Baltic  Sea  Action  Plan,  and  Estonian  Marine  Strategy.  However  there  is  a  lack  of 
quantitative assessment of the effects of these plans. For example, regarding the Nitrate 

Vulnerable Zone Action Plan it is only stated that its main objective is to help achieve 
the  main  objective  set  by  the  RBMPs  –  to  achieve  or  preserve  the  good  status  of  the 

water  bodies  and  ensure  safe  drinking  water  for  people  –  but  there  is  no  further 
quantitative  assessment  of  how  this  action  plan  supports  the  implementation  of 

RBMPs. Regarding the measures of the Baltic Sea Action Plan the relevant measures 
are included and integrated in the Programmes of Measures of the RBMPs, according 

to  their  relevance  in  specific  water  bodies.  These  measures  focus  on  wastewater 
treatment  (improvement  of  nitrogen  and  phosphorus  removal)  but  there  is  no 

quantitative  assessment  of  their  contribution.  It  is  just  stated  that  the  objective  of  the 
planned  measures  is  to  ensure  the  good  status  and  sustainability  of  the  marine 

132 

 
environment  of  the  Baltic  Sea.  The  same  conclusion  goes  for  the  Estonian  Marine 

Strategy  –  the  objective  has  been  presented,  but  no  quantitative  assessment  has  been 
done.  

This recommendation is partially fulfilled. 

  Recommendation: Provide complete information on the level of compliance, and timing 
to  reach  compliance,  by  agglomerations,  including  information  on  funding,  in 
accordance with Directive 91/271/EEC (article 15 and following). 

Assessment:  Measures  to  tackle  urban  point  sources  are  reported  in  WISE  for  all 
RBDs. 

Information  associated  with  the  Urban  Waste  Water  Treatment  Directive55  in  the 
RBMPs  is  rather  general.  It  is  mentioned  that  additional  investments  in  wastewater 

treatment  (construction  and  rehabilitation  of  sewage  systems  and  urban  wastewater 
treatment plants) are needed, even beyond the scope of PoM, to ensure compliance with 

other  Directives  and  national  requirements.  According  to  the  RBMPs,  increases  in 
pollution  charges  (a  roughly  10  %  increase  in  fees  each  year)  have  had  an  impact 

because  after  upgrade  the  wastewater  treatment  systems  have  become  considerably 
more  effective,  mainly  due  to  investments  made.  The  cost  of  the  measures  and  the 

deadlines  for  implementation  are  said  to  be  specified  in  the  separate  action  plan 
designated for PoM implementation, and possibly therefore the level of compliance and 

timing to reach compliance are not addressed in detail within the Estonian RBMPs. It is 
stated  in  the  RBMPs  that  for  a  number  of  measures  it  can  be  expected  that  their 

implementation  will  continue  in  the  third  cycle.  Surface  water  bodies  associated  with 
pressures  from  urban  wastewater  treatment  plants  have  generally  extended  deadlines 

for achieving environmental objectives. For example there are 61 of 105 water bodies 
in West-Estonian with an extended deadline of 2027, mostly due to their current poor 

ecological  status.  From  the  105  water  bodies  associated  with  urban  wastewater 
treatment plant pressure in the West-Estonian RBD, 24 do not comply with the permit 
requirements, mostly due to phosphorus. The corresponding numbers are higher in the 
East-Estonian RBD, with 91 of 131 water bodies having an extended deadline of 2027.  

Funding  for  these  measures  is  foreseen  to  come  from  the  state  budget,  from  local 
governments, European Union funds or from the private sector. 

Overall this recommendation is partially fulfilled. 

55  Council  Directive  91/271/EEC  of  21  May  1991  concerning  urban  waste-water  treatment  http://eur-
lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:31991L0271 

133 

 
 
                                                      
Topic 13 Measures related to hydromorphology  

13.1.  Assessment  of 

implementation  and 

compliance  with  WFD 

requirements in second cycle 

Significant hydromorphological pressures are identified only for rivers in the 3 RBDs. Except 

for a few water bodies affected by continuity barriers due to hydropower, all other significant 
hydromorphological  pressures  are  not  assigned  to  one  of  the  specified  sectors  according  to 

WISE (sector is reported as “other”). 

Operational KTM to address these pressures are clearly identified and include KTM5, KTM6, 
KTM7  as  well  as  research  activities  (KTM14).  Based  on  the  national  PoM,  although 

hydromorphological  measures  are  planned,  in  many  cases  they  are  not  specifically  described 
but presentations remain generic. This is largely due to the fact that many of the measures are 

of  investigative  nature  or  are  not  related  to  concrete  projects  yet.  Overall,  the  information 
provided  gives  evidence  for  the  following  types  of  measures  being  planned:  continuity 
measures  (fish  ladders,  by  pass  channels,  removal  of  structures  especially  of  beaver  dams), 

habitat  restoration,  sediment  management,  re-meandering,  setting  of  ecological  flows,  and 
dredging minimisation. 

In  terms  of  basic  measures,  there  is  an  authorisation  and/or  permitting  regime  in  place  to 

control physical modifications in all RBDs, which covers changes to the riparian area of water 
bodies according to WFD Article 11(3)i. There is also a register  of physical modifications of 

water bodies. 

Overall  management  objectives  and  quantitative  objectives  in  terms  of  restoring  river 
continuity have been set in all three RBDs. 

Win-win  measures  in  terms  of  achieving  the  objectives  of  the  WFD  and  Floods  Directive, 
drought management and use of Natural Water Retention Measures are included in the PoM of 
all  three  RBDs,  but  KTM23  on  Natural  Water  Retention  Measures  is  not  reported  as 
operational to tackle any significant pressures. 

The design of new and existing structural measures, such as flood defences, storage dams and 

tidal barriers, has not been adapted to take into account WFD objectives. 

Ecological  flows  have  been  derived  for  all  relevant  water  bodies  in  all  three  RBDs.  Their 
implementation  is  partial  as  derived  ecological  flows  have  only  been  implemented  for  some 

134 

 
water bodies, but relevant work is still ongoing. Based on the PoM, the specific measures for 

achieving ecological flows are planned to be implemented in the second cycle (2016-2021).  

Specific measures for achieving ecological flows are planned specifically in the East-Estonian 

RBD  for  the  Narva  river  with  the  aim  to  direct  water  from  the  Narva  reservoir  back  to  the 
natural  river  bed  and  ensure  the  ecological  minimum  flow.  In  order  to  ensure  the  ecological 

flow  and  water  regime  of  the  water  body  on  the  expanded  river  section,  relevant  permit 
conditions are established, supervised and monitored. This type of measure (of administrative 

nature) is planned and implemented for many of the water bodies in all three RBDs. It should 
be noted that in the Estonian context this particular measure is not explicitly assigned as basic 

measure  (imposing  controls  on  uses  impacting  the  flow  regime),  but  as  a  planned  additional 
measure. 

Indicators on the gap to be filled for significant hydromorphological pressures and KTM value 

indicators are reported for 2015 and 2021. Information provided in the WISE reporting shows 
that  there  will  be  considerable  progress  in  closing  the  gap  by  2021  in  terms  of  all  types  of 

significant  hydromorphological  pressures  (physical  and  hydrological  alterations,  continuity 
barriers).  Information  from  the  second  RBMPs  though  indicates  that  many  exemptions 

(extended deadline) set for 2027 are associated with migration barriers and therefore measures 
to improve fish migration. 

Depending  on  the  measure,  the  financing  of  measures  is  foreseen  from  state  budget,  local 
authorities, the European Union and from the private sector. From the information provided in 

the  national  PoM,  though,  it  seems  overall  unclear  for  which  measures  a  budget  is  clearly 
allocated in the second RBMPs. 

13.2.  Main changes in implementation and compliance since first cycle 

A major improvement seems to be that a number of hydromorphological measures are clearly 
reported  as  operational  (KTM5,  KTM6,  KTM7)  to  address  significant  hydromorphological 
pressures in  the second  RBMPs, while in  the first  RBMPs, no hydromorphological  measures 
had been identified by the time of the adoption of the plans. According to information in the 

second RBMPs, hydromorphological measures have become more specific in the second cycle 
compared  to  general  indications  in  the  first  cycle.  However,  several  measures  are  still  not 

specifically described and presentations remain generic; specific information on the technical 
measures is provided only for some water bodies. 

135 

 
13.3.  Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first PoM requested action 
on the following: 

  Recommendations:  “Ensure  that  its  ecological   flow  methodology  is  compatible  
with  Good  Ecological  Status (GES), and that it takes into account the CIS guidance 
that has been adopted.” "  

Assessment:  Although  ecological  flows  are  reported  to  have  been  derived  for  all 
relevant water bodies in all three RBDs, the RBMPs do not present any information on 
the  Common 
an  updated  ecological  flow  methodology  or 

to  having  used 

Implementation  Strategy  guidance  on  ecological  flows.  Therefore,  based  on 
information found, the recommendation on updating the ecological flow methodology 

has not been fulfilled. 

  Recommendation: “Consider  and  prioritise  the  use  of  green  infrastructure  and/or  
  retention  measures  that  provide  a  range  of  environmental 

  water 

natural 

(improvements  in  water  quality,  flood  protection,    habitat    conservation  etc.),social  
and  economic  benefits  which  can  be  in many cases more cost-effective than grey 

infrastructure”   

Assessment:  The  WISE  reporting  indicates  that  no  natural  water  retention  measures 

(KTM23) are made operational to tackle significant pressures. In addition, no reference 
is  found  in  any  of  the  RBMPs  on  a  national  or  regional  strategy  that  prioritises  the 

implementation of natural water retention and green infrastructure measures. Therefore, 
this recommendation has not been fulfilled. 

136 

 
 
 
Topic 14 Economic analysis and water pricing policies  

14.1. Assessment  of 

implementation  and  compliance  with  the  WFD 

requirements in the second cycle 

The definition of water services has been expanded to  include abstraction uses. These "new" 

water services are associated to abstraction in a wider sense, but narrowly speaking are divided 
into abstraction in industry, abstraction in mining, abstraction in agriculture, and abstraction in 

electricity  production  (cooling  water).  Hydro-energy  generation  is  not  defined  as  a  water 
service. 

For the water services, it is stated that the level  of financial cost recovery is at 100 %  (apart 

from  households/sewage  where  it  is  86%  on  average);  however,  environmental  costs  are  not 
covered. It is not  clear whether the calculations of cost  recovery have changed from the first 

cycle. 

A contribution to cost recovery is assured for at least households, industry and agriculture; it is 

however  not  clear  whether  the  contribution  is  adequate.  Other  water  uses  are  defined,  but 
without a link to Article 9 of the WFD.  

It was reported to WISE that no uses contribute to cost recovery. 

Environmental  and  resource  costs  are  calculated  as  in  the  first  cycle,  but  reported  as  only 
partially  covered  by  existing  pricing  mechanisms  (pollution  charges  and  the  tax  for  water 

resource  use)  and  that  more  analysis  is  needed  for  determining  the  total  costs  and  needs  for 
additional financial coverage. 

The economic analysis is reported as having been updated. 

14.2. Main changes in implementation and compliance since the first cycle 

It  can  be  deduced  that  some  information  has  been  updated  (e.g.  "expansion"  of  the  water 

services definition though inclusion of a number of "self-services") and the economic analysis 
is reported as having been updated. 

14.3. Progress with Commission recommendations 

The Commission recommendations based on the first RBMPs and first  PoM requested action 
on the following: 

137 

 
  Recommendation:  Estonia  should  ensure  the  application  of  broad  definition  of  water 
services for the purpose of Article 9 implementation by inclusion of water abstraction 
for inter alia hydro-energy generation. Estonia should assure adequate contribution to 

cost-recovery  of  different  water  uses  disaggregated  at  least  into  households,  industry 
and agriculture. 

Assessment: A broader definition of water services is used than in the first cycle. Based 

on the RBMPs the "new" water services are associated to abstraction in a wider sense, 
but  narrowly  speaking  are  divided  into  abstraction  in  industry,  abstraction  in  mining, 

abstraction  in  agriculture,  and  abstraction  in  electricity  production  (cooling  water). 
However, abstractions seem not to be regarded as separate uses/services, but as part of 

industry and agriculture; the across-the-board determination of cost recovery rates for 
these  services  at  100  %  hints  at  a  flat  assessment/treatment  of  abstractions. 

Additionally, abstractions for hydro-energy generation are not included. 

For the water services, it is stated that the level of financial cost recovery is at 100 % 

(apart  from  households/sewage where it is  86%  on average); however,  environmental 
costs are not recovered. The contribution is not disaggregated into households, industry 

and agriculture. 

Other activities linked to significant pressures not considered as water services and not 
reported as exempted under Article 9(4) (in particular, these are presented as significant 

water uses based on Article 4 and Annex III of the WFD) are: 

a.  Diffuse pollution from agriculture: mainly nutrient pollution from farmland and 

manure storage facilities. 

b.  Diffuse pollution from  forest  drainage areas:  Forest  drainage involves nutrient 

pollution and the transfer of nutrients to water bodies. 

c.  Pollution from rainwater in densely populated areas: point and diffuse pollution 

of hazardous and priority substances and the transfer of nutrients. 

d.  Residue pollution (industrial sites, landfills, etc.): point and diffuse pollution of 

hazardous and priority substances and the transfer of nutrients. 

e.  Hydromorphological pressure associated with drainage of arable lands. 

138 

 
f.  Beaver  dams  on  the  rivers:  The  environmental  pressure  of  beaver  dams  is  the 
hydromorphological pressure on the rivers. Landowners are responsible for the 
removal of beaver dams. 

g.  Fish  farming:  causes  environmental  pressure  through  the  transfer  of  nutrients 

from fishponds. 

h.  Water use for hydropower production. 

i.  The  presence  of  dams  and  other  blocking  facilities  on  rivers  not  related  to 

hydropower. 

Other activities are linked to significant pressures not considered as water services and without 

a contribution to cost recovery (see above). 

A contribution to cost recovery is assured for at least households, industry and agriculture; it is 

however not clear whether the contribution is adequate. Hence, the recommendation has been 
partly fulfilled. 

In  the  three  RBMPs  it  is  not  always  possible  to  clearly  differentiate  environmental  and 

resource costs from one another. 

With  regard  to  environmental  and  resource  costs,  the  explanation  is  provided  that 

environmental costs are currently partially covered by existing pricing mechanisms (pollution 
charges and the tax for water resource use) and that more analysis is needed for determining 

the total costs and needs for additional financial coverage.  

According  to  the  RBMPs,  the  number  of  water  bodies  for  which  the  achievement  of 

environmental  objectives  is  in  danger  increases  due  to  the  pressure  and  extent  of  water  use. 
Therefore,  an  economic  analysis  was  carried  out  to  assess  the  environmental  impact  of  the 

pressure  of  water  use,  and  then  a  compensatory  mechanism  was  found  and  described  to 
compensate for these costs through additional measures. 

Environmental  and  resource  costs  seem  to  be  estimated  quantitatively  based  on  the  costs  of 
these measures, using the same approach as in the first cycle (no changes reported). 

In conclusion, there is partial progress on this recommendation. 

139 

 
 
 
Topic 15 Considerations specific to Protected Areas (identification, 
monitoring, objectives and measures) 

15.1. Assessment  of 

implementation  and  compliance  with  the  WFD 

requirements in the second cycle 

Information is provided for surface water protected areas related to all relevant Directives and 
for groundwater dependent protected areas under the Habitats56 and Birds57 Directives (Table 
15.1). The same applies to nitrate vulnerable58 groundwater areas. 

Table 15.1  Number of Protected Areas of all types in each RBD of Estonia,  for surface 

and groundwater 

Protected Area type 

Abstraction of water intended for 
human consumption under 
Article 7 

Recreational waters, including 
areas designated as bathing 
waters under Directive 
76/160/EEC59 

Protection of species where the 
maintenance or improvement of 
the status 
of water is an important factor in 
their protection, including 
relevant Natura 2000 sites 
designated under Directive 
79/409/EEC (Birds)60 

Protection of habitats or species 
where the maintenance or 
improvement of the status 
of water is an important factor in 
their protection, including 
relevant Natura 2000 sites 

Number of Water Bodies Associated with 

Rivers 

Lakes 

Transitional 

Coastal 

Groundwater 

2 

18 

1 

9 

2360 

26 

62 

30 

3 

26 

15 

263 

62 

3 

82 

42 

56  Council  Directive  92/43/EEC  of  21  May  1992  on  the  conservation  of  natural  habitats  and  of  wild  fauna  and 
flora http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:31992L0043 
57Directive  2009/147/EC  of  the  European  Parliament  and  of  the  Council  of  30  November  2009  on  the 
conservation of wild birds http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32009L0147 
58  Council  Directive  91/676/EEC  of  12  December  1991  concerning  the  protection  of  waters  against  pollution 
caused 
http://eur-lex.europa.eu/legal-
agricultural 
content/EN/TXT/?uri=celex:31991L0676 
59  Directive  2006/7/EC  of  the  European  Parliament  and  of  the  Council  of  15  February  2006  concerning  the 
management  of  bathing  water  quality  and  repealing  Directive  76/160/EEC  http://eur-lex.europa.eu/legal-
content/EN/TXT/?uri=CELEX:32006L0007  
60  Directive  2009/147/EC  of  the  European  Parliament  and  of  the  Council  of  30  November  2009  on  the 
conservation of wild birds http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32009L0147  

sources 

nitrates 

from 

by 

140 

 
 
 
 
 
                                                      
Protected Area type 

designated under Directive 
92/43/EEC (Habitats)61 

Nutrient-sensitive areas, 
including areas designated as 
vulnerable zones under Directive 
91/676/EEC and areas 
designated as sensitive areas 
under Directive 91/271/EEC 

Areas designated for the 
protection of economically 
significant aquatic species (fish 
and shellfish) 

Other 

Number of Water Bodies Associated with 

Rivers 

Lakes 

Transitional 

Coastal 

Groundwater 

1 

1 

109 

1 

3 

Source: WISE electronic reporting  

No  information  is  provided  for  groundwater  Drinking  Water  Protected  Areas62  (Table  15.2). 
There was a substantial number of monitoring sites (127) for groundwater identified Drinking 

Water  Protected  Areas  in  the  first  cycle  and  these  sites  have  also  been  left  out  of  the  status 
assessment for the second cycle63.  

A new delineation of groundwater bodies has been carried out leading to an increased number 
of groundwater bodies since the first cycle. Groundwater bodies have been subdivided and new 

groundwater  bodies  have  been  formed.  It  is  explained  that  the  aim  of  establishing  a  larger 
number of smaller groundwater bodies is to better organize the protection of their chemical and 

quantitative status. 

No status assessment of groundwater Drinking Water Protected Areas has been reported. For 
both  quantitative  and  qualitative  status  (Figure  15.1),  relatively  few  Nitrates,  Habitats  and 

Birds  protected  areas  related  to  groundwater  have  been  reported  -  in  general  with  low 
confidence  which  corresponds  to  the  missing  monitoring  specifically  for  groundwater 

protected areas. 

61  Council  Directive  92/43/EEC  of  21  May  1992  on  the  conservation  of  natural  habitats  and  of  wild  fauna  and 
flora http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:31992L0043  
62  Council  Directive  98/83/EC  of  3  November  1998  on  the  quality  of  water  intended  for  human  consumption 
https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX%3A31998L0083  
63 Estonia subsequently clarified that this was a reporting error and that according to the reporting manual (Article 
7 of the WFD requires Member States to establish drinking water protected areas for bodies of groundwater and 
surface water providing more than 10 m3 a day as an average or serving more than 50 persons, or for bodies that 
are intended for that use in the future. The objective for these areas is to avoid deterioration in quality in order to 
reduce the level of purification treatment required) there are 39 of these areas. 

141 

 
 
 
 
 
 
 
 
 
 
 
 
                                                      
 
Figure 15.1  Status of water bodies associated with the Protected Areas report for Estonia. 

NB - based on status/potential aggregated for all water bodies associated with 
all Protected Areas. 

Source: WISE electronic reporting 

For  surface  water  protected  areas,  a  comprehensive  status  report  has  been  delivered  (Figure 
15.1). In general, the confidence of the status assessment is either high or low - and this is also 
the case for the different types of protected  areas except for bathing water areas64, where the 
confidence in general is high.  

This lack of monitoring specifically related to all types of protected areas might not meet the 
WFD requirements. 

64  Directive  2006/7/EC  of  the  European  Parliament  and  of  the  Council  of  15  February  2006  concerning  the 
management  of  bathing  water  quality  and  repealing  Directive  76/160/EEC  http://eur-lex.europa.eu/legal-
content/EN/TXT/?uri=CELEX:32006L0007 

142 

 
 
 
 
                                                      
Only  some  types  of  protected  areas  –  Drinking  Water  Protected  Areas  (Article  7),  bathing 

waters,  habitats  and  nitrate  vulnerable  areas  have  been  incorporated  into  the  RBMPs.  This 
means that protected areas related to e.g. the Birds Directive or Urban Waste Water Treatment 
Directive65 are not included in the RBMPs. 

For  the  types  of  protected  areas  that  have  been  incorporated  in  the  RBMPs,  additional 

objectives  have  not  been  set  except  for  bathing  water  areas.  There  are  two  explanations  for 
this: 

1.  For groundwater dependent protected areas it is stated for both Birds and Habitat areas, 
that achieving good status for the groundwater is sufficient also to reach the favourable 

conservation status.  

2.  For all types of surface water protected areas it is stated that additional objectives have 

not been set because additional needs are not known. 

It is possible that a “default” approach has been used, and is not based on an assessment of the 
individual protected area. If this is the case it might not meet the requirements in the WFD. 

Table 15.2  Number of monitoring sites associated with Protected Areas in Estonia  

Protected Area type 

Number of monitoring sites associated 
with Protected Areas in 

Ground-
water 

Lakes 

Rivers 

Protection of habitats or species where the maintenance or 
improvement of the status of water is an important factor in their 
protection, including relevant Natura 2000 sites designated under 
Directive 92/43/EEC (Habitats) 
Nutrient-sensitive areas, including areas designated as vulnerable 
zones under Directive 91/676/EEC and areas designated as sensitive 
areas under Directive 91/271/EEC 

123 

Source: WISE electronic reporting 

Safeguard  zones  to  protect  drinking  water  have  been  implemented  with  a  differentiated  size 
approach depending on actual needs. It is not clear from the RBMPs what kind of restrictions 

are imposed in the safeguard zones. 

Exemptions have not been used for either groundwater or surface water. 

65  Council  Directive  91/271/EEC  of  21  May  1991  concerning  urban  waste-water  treatment  http://eur-
lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:31991L0271 

143 

 
 
 
 
 
 
 
 
 
 
 
                                                      
15.2. Main changes in implementation and compliance since the first cycle 

There  seems  to  be  a  significant  change  in  the  strategy  for  the  delineation  of  groundwater 
bodies resulting in an increased number of groundwater bodies. 

The monitoring activity related to protected areas appears to have changed considerably. In the 
first RBMPs, a rather comprehensive monitoring program was reported with activities for all 
relevant types of protected areas. No such data was reported in WISE in the second cycle66. 

15.3. Progress with Commission recommendations 

  Recommendation:  "Assess  the  requirements  of  Birds  and  Habitats  areas  and,  if 
additional  water  requirements  (quality/  quantity)  are  needed  to  achieve  favourable 
conservation status, and include them as additional objectives in the second RBMPs." 

Assessment: Objectives have not been set - either because the achievement of the good 
status  is  assessed  to  be  sufficient  to  reach  the  favourable  conservation  status 

(groundwater  dependent  habitat  and  bird  areas)  or  because  additional  needs  are  not 
known (surface water areas). It seems as if no assessment of each individual protected 

area has been made and that the reported information is more or less a default. There 
thus seems not to have been any progress in relation to this recommendation. 

66 Estonia has clarified that the additional monitoring in protected areas includes additional monitoring of drinking 
water  intakes  and  areas  of  water  affecting  the  quality  of  drinking  water,  and  the  monitoring  of  areas  of  water 
affecting  the  quality  of  bathing  areas  and  bathing  water.  Additional  water  monitoring  is  also  planned  for  areas 
where  the  conservation  or  improvement  of  water  status  is  a  significant  protective  technique.  Additional 
monitoring also includes monitoring of groundwater in nitrate-sensitive areas. The areas sensitive to nutrients are 
among  other  things  also  included  in  the  operational  monitoring  of  groundwater  bodies,  where  it  is  evaluated 
together with the impact of the pollution source. 

144 

 
 
 
                                                      
Topic 16 Adaptation to drought and climate change 

16.1. Assessment  of 

implementation  and  compliance  with  the  WFD 

requirements in the second cycle 

Climate change was considered in all RBDs and it is stated that the guidance on how to adapt 

to climate change (Common Implementation Strategy Guidance Document No. 24) was used. 
Climate  change  was  considered  for  flood  management  and  for  the  preferential  selection  of 

robust  adaptation  measures.  It  was  also  used  when  assessing  direct  and  indirect  climate 
pressures.  

KTM24 is not made operational to tackle any significant pressure and no national measures are 

mapped  against  KTM  24.  This  is  a  contradiction  to  the  reporting  as  Estonia  has  made  a 
preferential selection of robust adaptation measures. 

No specific sub-plans addressing climate change are reported.  

According to the 2012 Topic Report on Water Scarcity and Drought in RBMPs, droughts are 
not  relevant  for  the  country.  No  exemptions  have  been  applied  for  Estonia  following  Article 

4(6) due to prolonged droughts. 

No Drought Management Plans have been developed in Estonia. This situation is similar to the 

first cycle (Topic report on: Assessment of Water Scarcity and Drought aspects in a selection 
of European Union River Basin Management Plans). 

16.2. Main changes in implementation and compliance since the first cycle 

Climate  change  issues  were  not  discussed  in  the  first  RBMPs  but  have  been  included  in  the 
second cycle.  

No Drought Management Plans have been developed in Estonia. This situation is similar to the 
first  cycle  (see  Topic  report  on:  Assessment  of  Water  Scarcity  and  Drought  aspects  in  a 

selection of European Union River Basin Management Plans). 

16.3. Progress with Commission recommendations 

No  recommendations  were  made  by  the  Commission  regarding  drought  management  or 
climate change. 

145