COMMISSION STAFF WORKING DOCUMENT Third River Basin Management Plans Second Flood Hazard and Risk Maps and Second Flood Risk Management Plans Member State: Lithuania Accompanying the document REPORT FROM THE COMMISSION TO THE COUNCIL AND THE EUROPEAN PARLIAMENT on the implementation of the Water Framework Directive (2000/60/EC) and the Floods Directive (2007/60/EC) Third River Basin Management Plans Second Flood Risk Management Plans
Date: 2025-02-04
Institutions: Directorate-General for Environment, European Commission
Subjects: Lithuania, 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, 4.2.2025  SWD(2025) 28 final  COMMISSION STAFF WORKING DOCUMENT Third River Basin Management Plans   Second Flood Hazard and Risk Maps and Second Flood Risk Management Plans Member State: Lithuania Accompanying the document REPORT FROM THE COMMISSION TO THE COUNCIL AND THE EUROPEAN PARLIAMENT on the implementation of the Water Framework Directive (2000/60/EC) and the Floods Directive (2007/60/EC)   Third River Basin Management Plans  Second Flood Risk Management Plans {COM(2025) 2 final} - {SWD(2025) 13 final} - {SWD(2025) 14 final} - {SWD(2025) 15 final} - {SWD(2025) 16 final} - {SWD(2025) 17 final} - {SWD(2025) 18 final} - {SWD(2025) 19 final} - {SWD(2025) 20 final} - {SWD(2025) 21 final} - {SWD(2025) 22 final} - {SWD(2025) 23 final} - {SWD(2025) 24 final} - {SWD(2025) 25 final} - {SWD(2025) 26 final} - {SWD(2025) 27 final} - {SWD(2025) 29 final} - {SWD(2025) 30 final} - {SWD(2025) 31 final} - {SWD(2025) 32 final} - {SWD(2025) 33 final} - {SWD(2025) 34 final} - {SWD(2025) 35 final}  
 
 
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Country specific staff working document 

Lithuania 

ENVIRONMENT 

 
 
 
 
 
 
 
 
Content 

Content ................................................................................................................................................................................................... 2 

SECTION A: WATER FRAMEWORK DIRECTIVE .......................................................................................................................... 3 

1. General info, member state characterisation ............................................................................................................. 4 

2. Horizontal aspects ...................................................................................................................................................................... 9 

2.1 Governance ............................................................................................................................................................................ 9 

2.2 Characterization of River Basin District ................................................................................................................. 9 

3. Policy elements contributing to biodiversity and climate change adaptation ...................................... 12 

3.1 Surface Water: what is their ecological status or potential .................................................................... 12 

3.2 Hydromorphological changes and artificialization (HMWBs and AWBs) .......................................... 15 

3.3 Groundwater bodies - have they sufficient water – quantitative status ......................................... 16 

3.4 Protected Areas (identification, monitoring, objectives and measures) ........................................... 17 

3.5 What is being done to prevent/reduce hydromorphological pressures ............................................ 18 

3.6 What Lithuania is doing for abstractions and water scarcity ................................................................ 19 

3.7 Adaptation to climate change .................................................................................................................................. 19 

4. Policy elements contributing to zero pollution ........................................................................................................ 20 

4.1 Surface Water: what is their chemical status ................................................................................................. 20 

4.2 Groundwater Bodies: what is their chemical status .................................................................................... 24 

4.3 What Lithuania is doing to combat pollution from agriculture ............................................................. 25 

4.4 What Lithuania is doing to combat pollution from other sectors ....................................................... 26 

4.5  What  Lithuania  is  doing  to  combat  significant  pressures  –  overall  assessment  of  the 
Programmes of Measures .................................................................................................................................................. 27 

5. Exemptions and economics ............................................................................................................................................... 27 

5.1 To what extent are exemptions applied in Lithuania .................................................................................. 27 

5.2 Use of economic analysis and water pricing – cost recovery ................................................................ 29 

6. WFD recommendations ........................................................................................................................................................ 30 

SECTION B: FLOODS DIRECTIVE .................................................................................................................................................. 33 

7. Flood risk management under floods directive (FD) ............................................................................................ 34 

7.1 Flood hazard and risk maps ...................................................................................................................................... 34 

7.2 Flood risk management plans .................................................................................................................................. 35 

8. FD recommendations ............................................................................................................................................................ 37 

2 

 
 
 
SECTION A: 
WATER FRAMEWORK 
DIRECTIVE 

3 

 
 
 
1. General info, member state characterisation

Lithuania is a low-lying Baltic coastal country, with a terrestrial area of close to 62 643 km² and a 
marine area close to 6,400km². It has borders with Latvia, Belarus, Poland, and the Kaliningrad region 
of  Russia.  It  is  the  largest  of  the 
three  Baltic  states.  It  hosts  2.86 
million inhabitants with a density of 
45  inhabitants  per  km2  lower  than 
the  EU  average.  Lithuania  has  a 
moderate  continental  climate  with 
cold  winters  and  rainy  summers. 
Lithuania’s  96  km  of  coast  have  a 
unique  and  vulnerable  landscape, 
rich in natural  resources. The share 
of terrestrial protected areas is 17% 
of  the  national  territory,  well below 
the 
Lithuania’s 
average. 
agricultural  sector  is  characterised 
by  relatively  favourable  production 
conditions.  It  is  foreseen  that  the 
area  under  organic  farming 
in 
Lithuania  will  increase  by  half  and 
reach  almost  13%  by  2028.  The 
share of the population living in rural 
areas (56.2%) is one of the highest 
in the EU. Approximately 45% of the 
total area of the country is used for 
agriculture  and  largely  the  rest  are 
forests.

EU 

Reporting 

The deadline for reporting the 3rd RBMPs was in March 2022. The Commission and the EEA together 
with Member States developed an electronic reporting system in WISE (Water Information System 
for  Europe).  Its  use  was  voluntary.  Some  Member  States  used  it  to  fulfil  their  obligations,  others 
reported the plans in pdf format. The cut-off date for the WISE e-reporting was September 2023 and 
the MS were assessed based on the datasets available by this date.  

By September 2023 Lithuania submitted full electronic reporting and therefore the assessment is 
based on this dataset. 

Despite the cut off dates for the production of this report, reporting continued and, for the State of 
Water  report,  the  EEA  aggregated    the  results  available  by  July    2024  in  their  products  and 
dashboards available at WISE Freshwater web portal. 

4 

 
Changes in Status, Pressures, Exemptions & Measures 

Surface 
Water 
Bodies  

Trend (% good 
status/potential) 

100%

ECOLOGICAL 
STATUS 

50%

51,9%

36,4%

0%

2015 2021

Main Pressures & Changes & Exemptions 

Since the 2nd RBMPs, the ecological status of SWBs deteriorated from 51.9% to 36.4% in good (or better) status as more SWBs were downgraded 
from “good” to “moderate” status. All coastal and transitional water bodies fail the objective of a good ecological status. Lithuania’s confidence 
in classification is reported “low” for most of the water bodies classified to be in good ecological status or potential. Looking forward, Lithuania 
expects  50.8%  of  SWBs  to  reach  a  good  ecological  status/potential  by  2027.The  most  significant  pressure  on  surface  water  is  ‘diffuse  – 
agricultural’  followed  by  by  morphological  changes.  The  most  significant  impact  on  the  ecological  status  is  nutrient  pollution.  Nitrates  in 
Lithuania’s rivers are unfortunately steeply increasing, contributing also to the euthropication of the Baltic Sea. Lithuania has mapped several 
measures to reduce pressures on the ecological status of SWBs: KTM1 - Construction or upgrades of wastewater treatment plants; KTM2 - 
Reduce nutrient pollution from agriculture; and KTM5 - Improving longitudinal continuity (e.g. establishing fish passes, demolishing old dams); 
KTM 6 Improving hydromorphological conditions of water bodies other than longitudinal continuity; KTM7 - Improvements in flow regime and/or 
establishment of ecological flows. Lithuania has invoked Article 4(4) exemptions for all SWBs failing good ecological status, that is for 62.6% 
of SWBs based on “technical feasibility” and for 39.6% based on “natural conditions”. 

5 

 
 
 
99,0%

100%

50%

CHEMICAL 
STATUS 

0,3%

0%

2015 2021

94% of SWBs are reported in unknown status, while 5% of water bodies are in poor chemical status and less than 1% are in 
good chemical status. 5% are in good chemical status if one discounts the uPBTs mercury, PBDEs and PAHs. Lithuania expects 
that only 0.6% of its SWBs will achieve good chemical status by 2027.  There has been  a  steep reduction of SWBs in good 
chemical status, with only 0.3% being reported to reach objectives in 2021. This seems mainly due to a steep increase in SWBs 
reported in “unknown” status. Lithuania did not provide details or a justification on a change of approach that could explain 
this regrettable development. Data reported under the Nitrates Directive show that Lithuania has the largest proportion of 
river sites with average nitrate concentrations exceeding 5.6mg (NO3-N/l), namely 25% in 2019-21. Lithuania also has one of 
the highest proportions of significantly increasing trends of nitrates in surface water bodies (45%) (EEA, 2021). It would appear 
that the monitoring network did not improve, and also expert judgement is no longer used either to assess the chemical status 
of surface water. The spatial and temporal scale of monitoring was, it seems, insufficient to characterise the chemical status 
of SWBs in the 3rd RBMP. This is a regrettable setback compared to Lithuania’s 2nd RBMP and suggests non-compliance with 
basic requirements under the WFD.  Lithuania has mapped KTM1 - Construction or upgrades of wastewater treatment plants 
,  KTM  3  –  Reduce  pesticides  in  agriculture;  but  it  has  not  included  KTM4  -  Remediation  of  contaminated  sites  (historical 
pollution  including  sediments,  groundwater,  soil)  in  the  programem  of  measures.  Also,  Lithuania  has  not  mapped  KTM9  - 
Water pricing policy measures for the implementation of the recovery of cost of water services from households.  Lithuania 
invoked Article 4(4) exemptions for 5% of all SWBs failing good chemical status, for 1% of all SWBs due to technical feasibility 
and 5% due to natural conditions. 

Ground 
Water 
Bodies  

Trend (% good 
status/potential) 

Main Pressures & Changes & Exemptions 

6 

 
 
 
QUANTITATIVE 
STATUS 

All 20 GWBs are reported to be in a good quantitative status, as in the previous two RBMPs. This assessment is, however, subject to certain 
doubts as 25% GWBs are affected by saline intrusions and because Lithuania fails to consider groundwater associated surface waters and/or 
groundwater dependent ecosystems in three of four RBMPs for establishing the quantitative status of its GWBs. 70 % of all classifications 
are conducted with high confidence whereas there was still 100% high confidence in the previous RBMPs. No justification for this change was 
provided. Water scarcity is not considered an issue in Lithuania. No GWB is at risk of failing good quantitative status by 2027. 

CHEMICAL 
STATUS 

All 20 GWBs are reported to be in good chemical status similarly to the 2nd RBMPs despite 25% GWBs being affected by saline intrusions. 
Regrettably,  the  number  of  surveillance  monitoring  sites  for  the  20  GWBs  decreased  from  278  (2015)  to  189  (2021).  Only  70%  of 
classifications are still conducted with high confidence, down from 100% (2015). There are also gaps in the assessment methodology and 
implementation including pharmaceuticals carbamazepine, sulfamethoxazole, and primidone in monitoring. No groundwater body is reported 
at risk of failing a good chemical status by 2027. This is a pronounced difference to the chemical status of Lithuania’s surface water bodies 
where only 0.6% of SWBs are expected to achieve a good status by 2027. The status of groundwater being influenced by the status of surface 
waters,  one  would  normally  expect  that  Lithuania’s  groundwater  are  also  affected  by  chemical  and  nutrient  pollution  in  rivers,  which 
interestingly does not seem to be the case. All of Lithuania’s drinking water stems from groundwater.  

7 

 
 
 
 
 
2. Horizontal aspects 

2.1 Governance 

The  main  authority  competent  for  implementing  the  Water  Framework  Directive  (WFD)  is  the 
Environmental Protection Agency (part of the Lithuanian Ministry of Environment). 

Lithuania also undertakes transboundary surface water body status assessments with Poland and 
Latvia,  which  is  a  good  administrative  practice.  There  are  no  transboundary  groundwater  bodies 
reported in Lithuania. Transboundary cooperation with the Russian Federation and the Republic of 
Belarus has ended after Russia’s invasion of Ukraine. 

As regards the coordination with the Marine Strategy Framework Directive (MSFD), it is noted very 
positively  that  all  of  Lithuania’s  RBMPs  provide  information  about  the  coordination  of  the 
implementation  of  the  WFD  and  the  MSFD.  The  second  objective  of  Lithuania’s  National  Water 
Development Plan 2022-2027 is to achieve and/or maintain good environmental status in the Baltic 
Sea. A priority is to reduce pollution reaching the Baltic Sea and the Curonian Lagoon through river 
runoff. Lithuania is cooperating on the protection of the Baltic marine environment in the HELCOM. 

As regards the coordination with the Flood Directive (FD), a joined consultation was organised on the 
RBMPs  and  FRMPs  and  all  of Lithuania’s  RBMPs provide information  on  the  coordination  with  the 
Flood  Risk  Management  Plans  (FRMP)  and  equally  they  integrate  WFD  and  FD  objectives  in  their 
Programme of Measures.  

2.2 Characterization of River Basin District 

Lithuania has four River Basin Districts, which are all  international, that means shared with other 
countries namely Latvia, Poland, Belarus, and the Russian Federation. The biggest RBD is Nemunas 
(LT1100)- covering almost 75% of the country- followed by Lielupe (LT3400), Venta (LT2300), and 
Dauguva (LT4500). All four RBDs in Lithuania are also international river basin districts (IRBD). The 
Nemunas RBD covers the part of the Nemunas River Basin in Lithuania, the Lithuanian coastal River 
Basin, a small part of the Pregolya RB (RU), the Lithuanian part of the Curonian Lagoon (transitional 
waters),  and  the  Baltic  Sea  (coastal  waters).  The  Lielupe  RBD  covers  14%,  Venta  RBD  10%  and 
Dauguva RBD 2% of the country’s territory. The share of Lithuania in the respective international 
RBDs is 50% (Nemunas), 49.1% (Lielupe), 27.4% (Venta) and 2.2% (Dauguva). 

The delineation of waterbodies has remained very stable from the previous cycle to this one. The 
number of Surface water bodies (SWBs) remained almost unchanged (from 1186 in the 2nd RBMPs 
to 1194 SWBs in the 3rd RBMPs). One river body was added to each RBD and there was also a 1.1 % 
increase in the number of lake bodies in the Lielupe and Dauguva RBDs. The numbers of transitional, 
coastal, and territorial water bodies remained the same. The number of groundwater bodies remained 
the same in all RBDs. Compared to the 2nd RBMPs, there has been no change in the number of artificial 
water bodies and heavily modified lakes. Only the number of heavily modified river water bodies has 
decreased by one, from 244 to 243. 

8 

 
 
 
Table 1. Number of surface water bodies and groundwater bodies per RBD in Lithuania 

Rivers 

Lakes 

Transitional 
waters 

Coastal 
waters 

Territorial 
waters 

Groundwater 
bodies 

RBD 
(index) 

Nemunas 

LT1100 
Venta 

LT2300 

Lielupe 

LT3400 

Dauguva 
LT4500 

583 

285 

96 

129 

18 

20 

20 

36 

4 

0 

0 

0 

4 

2 

0 

0 

0 

2 

1 

0 

0 

0 

1 

12 

1 

5 

2 

20 

TOTAL 

826 

361 

Source: WISE e-reporting 

Lithuania has established reference conditions for rivers and for lakes. Moreover, it has established 
the ecological status indicator values for biological quality elements in all water categories, except 
for benthic fauna and fish in transitional waters. Furthermore, type-specific reference conditions have 
been established for some hydromorphological quality elements in all rivers and lakes and in 67% 
of  transitional  waters.  Type-specific  reference  conditions  have  also  been  established  for  some 
physico-chemical quality elements in all rivers, lakes, transitional and coastal waters.  

Pressures on surface waters  

It is noted with concern that in this cycle, Lithuania reported significantly more SWBs under pressure 
than before, for both ecological and chemical pressures. Regrettably, in the 2nd RBMPs less than half 
of the SWBs were under pressure (48%), while in the 3rd RBMPs all SWBs are under pressure. This is 
coupled with the finding that Lithuania cannot identify the anthropogenic pressure for almost half of 
the SWBs (42%), compared to only 3% in the 2nd RBMPs. The problem seems to be caused largely 
by pressures from diffuse sources which increased from 3% in the 2nd RBMPs to 42% of the SWBs 
in the 3rd RMBPs. 

The most significant impact on SWBs is nutrient pollution, affecting 38% SWBs (up from 26% in the 
2nd RBMPs), followed by morphological changes (from 11% up to 27%) and organic pollutants (from 
9% to 14%). Regrettably, for as much as 36 % of all SWBs the impacts remain still ‘unknown’.  

The agricultural sector bears the major share of nitrate and nitrogen pollution in water bodies and is 
also causal to phosphates pollution.  

Nitrates pollution  of Lithuania’s  surface  water bodies,  as  reported  under  the Nitrates Directive,  is 
moderate.  18%  of  monitoring  stations  reported  nitrates  concentrations  below  10  mg/l  and  9% 
reported above 10 mg/l. Both population and cattle density are relatively low. Nitrates concentration 
is, however, high along Lithuania’s coast of the Baltic Sea.  That said, there is an upward trend of 
nitrates in Lithuania’s rivers. The EEA reports that in 2021 Lithuania had the largest proportion of 
river sites with average nitrate concentrations exceeding 5.6mgNO3-N/l (25%) as well as the highest 
proportion of significantly increasing trends (45%).1 

1 EEA, Ntrients in Freshwater in Europe, 2021. 

9 

 
 
Figure 1. Trophic status in Lithuania as per the Nitrates Directive 

 Source: Joint Research Center of European Commission (n.d.). JRC NITRATES DIRECTIVE  - Reporting Period 7 (2016-

2019) 

Trophic 

Status. 

[online] 

water.jrc.ec.europa.eu. 

Available 

at: 

https://water.jrc.ec.europa.eu/portal/apps/dashboards/cb6034c2a75e4df282f8a62f90c16caa   

Note : 0% of the monitoring stations are above the threshold of 50mg/l  

Based on data from 2014-2018 displayed by the Lithuanian Environmental Protection Agency, a gap 
analysis2 exists for nitrogen, phosphorus, nitrate, and phosphates pollution. The data also break down 
required reduction loads per sector, a good practice of transparency. The agricultural sector causes 
by far the largest pollution with nitrates (92%) and nitrogen (94%) while significantly lower loads fall 
on agriculture for phosphorus (56%) and phosphates (42.6%) and more efforts will be needed from 
wastewater treatment plants (31% phosphorus and 41% phosphates).  

Waste  water  treatment:  99%  of  Lithuania’s  sewage  is  treated  in  line  with  EU  legislation24  in 
particular with the Urban Waste  Water Treatment Directive. Yet Lithuania’s gap  analysis suggests 
that 490.27 kilometres of water bodies in two of three RBDs are affected by diffuse urban run-off 
that  is  preventing  the  achievement  of  objectives.  Point  source  pollution  from  urban  waste  water 
treatment plants prevents 110 water bodies from achieving objectives across all RBDs.27   

As  regards  hydroelectricity,  there  are  over  90  small  hydropower  plants,  together  with  the  Kauno 
Algirdo Brazausko hydropower plant (100 MW)  and the Kruonis pumped storage plant (800 MW). 
Depending on the water levels, these hydropower plants can generate over 100 GWh of electricity 
per year to a large extent coming from the river Nemunas. 

2 Detail data can be found in infographics, tables and maps: 
https://vanduo.old.gamta.lt/files/ataskaita.html#rezultatų-santrauka.  

10 

 
 
 
Like in other countries, the establishment of invasive alien species is also hampering the achievement 
of  a  good  ecological  status.  In  Lithuania,  there  are  four  species  of  crayfish,  some  of  which  are 
considered alien and invasive.3 These can cause significant harm to the riverbanks and other species.  

Pressures on groundwaters 

In the 2nd RBMPs, ‘no significant impacts’ were reported for 100% GWBs. Yet, just as for surface 
waters,  Lithuania  identifies  many  more  pressures  on  groundwater  bodies  compared  to  the  2nd 
RBMPs. In this cycle, pressures are reported from public water supply (25%), diffuse pressures from 
discharges not connected to a sewerage network (20%), pressures from urban run-off (20%) and 
diffuse pressures from transport (15% GWBs). Furthermore, Lithuania reports for the first time that 
25% of GWBs are affected by saline or other intrusions.     

As regards abstractions, water abstractions dropped significantly after Lithuania phased out nuclear 
power  generation  in  2009.  Since  then,  most  water  is  being  abstracted  for  cooling  thermal  power 
plants to produce electricity (90.9%), households and services (5.4 %), aquaculture (1.9 %), industry 
(1.8%) and agriculture (0.1 %).  

Water abstractions seem to be increasing in agriculture, households, and services and in industry. The 
abstraction of water is generally not identified as a significant pressure on water bodies in Lithuania, 
similarly to the 2nd RBMPs.  

Figure 2. Evolution of water abstractions in Lithuania 2000-2019 (EEA) 

Source: EEA Water Abstractions by economic sector 2000- 20194 

3 “A Comparative Study of Physiological and Biochemical Indices of Native European and Alien Species of Crayfish in 
Lithuania: https://www.astacology.org/article.asp?uid=Guest&a=568&t=1&type=1. 
4 Conventional statistic abstraction data of Eurostat, EEA and OECD exclude water disappearing after abstraction via 
leakages or evaporation from the surfaces of reservoirs and canals. Leakage and evapotranspiration losses can however be 
significant in MSs with many reservoirs and/or older distribution systems, as is illustrated by French data. Page 14, French 
analytical note on total water consumption (incl. evapotranspiration and losses) adding up to 54.000 million m3 abstracted, 
instead of 30.000 million m3 used: https://www.strategie.gouv.fr/sites/strategie.gouv.fr/files/atoms/files/fs-2024-
na_136_enjeux_et_usages_de_leau_avril.pdf 

11 

 
 
 
3. Policy elements contributing to biodiversity and 

climate change adaptation 

3.1 Surface Water: what is their ecological status or potential 

Monitoring 

The entire monitoring network of water bodies consists of 1073 sites. In rivers, fewer monitoring 
sites are included in the surveillance monitoring program (192) than in the operational monitoring 
program (489)5. The opposite applies to lakes with 224 and 131 sites, respectively. For transitional 
and  coastal  waters,  16  and  15  operational  monitoring  sites  are  reported,  but  no  surveillance 
monitoring sites. In coastal and transitional water bodies within the Nemunas RBD, morphological 
changes, hydrological or tidal regimes are monitored.  

There  is  a  nuanced  picture  on  the  progress  on  monitoring.  Compared  to  the  2nd  RBMPs,  the 
monitoring increased for some quality elements, especially biological quality elements. It is noted 
positively  that  in  the  3rd  RBMPs,  monitoring  includes  new  biological  quality  elements  such  as 
phytobenthos  for  lakes,  phytoplankton  for  rivers,  macrophytes,  phytobenthos,  and  benthic 
invertebrates for transitional waters, and macrophytes and phytobenthos for coastal waters. Equally 
welcome is the fact that monitoring of transparency conditions and nitrogen conditions for lakes and 
oxygenation  conditions  for  rivers  have  increased.  However,  on  the  contrary  there  has  been  less 
monitoring for some quality elements in rivers and lakes for physico-chemical quality 6￼. Similarly, 
monitoring of phosphorus conditions in lakes and rivers has decreased slightly, from 99% to 92% 
and  100%  to  99.8%,  respectively.  While  the  nutrients  conditions  are  monitored  very  well,  many 
physico-chemical quality elements, in particular for transitional and coastal water bodies, are still not 
monitored at all or not sufficiently. Salinity conditions, thermal conditions and acidification status are 
not monitored at all for all types of surface water bodies (SWBs). Oxygenation conditions are only 
monitored in rivers. Transparency conditions are only monitored in lakes and coastal water bodies. 

Lithuania’s electronic reporting under the 3rd RBMPs also suggests that in practice Lithuania only 
monitors RBSPs in 5% of its rivers and not at all in lakes. It is also noted that since the 2nd RBMPs 
(2016),  Lithuania  no  longer  uses  expert  judgment  to  close  data  gaps  for  RBSPs,  or  data  gaps 
regarding the hydrological regime or the morphological conditions of rivers. Most of the time, RBSP 
were monitored at a frequency equal to or above the minimum frequency (four times per year).7  

Status Assessment 

5 There are two types of monitoring: i) operational monitoring to determine the status and which covers all water bodies 
at risk and ii) surveillance monitoring aimed rather at identifying impacts and long-term changes. Lithuania has reported 4 
types of monitoring: intensive and extensive surveillance monitoring, operational monitoring, and investigative monitoring. 
6 The Republic of Lithuania subsequently explained that oxygenation conditions are monitored in lakes, fish are not 
monitored in coastal waters, and that hydrological regime and morphological conditions are monitored in 100% of 
coastal waters. Moreover, fish, hydrological regime, and morphological conditions are monitored in 75%, 100%, and 
100% of all transitional water bodies respectively. Additionally, all general physico-chemical quality elements are 
monitored in all coastal and transitional water bodies. Finally, further concerns were raised about the accuracy of the 
data on the salinity conditions and the acidification status for lakes and rivers, but no further details were provided. 
7 RBSP were monitored at 38 river water bodies with 48 sites, 1 lake was monitored with 1 site, 2 coastal waters were 
monitored with 5 sites, 4 transitional waters were monitored with 16 sites. 

12 

 
 
The 3rd RBMPs explain how the river basin specific pollutants (RBSPs) have been identified and how 
they are used for classifying surface water bodies according to ecological status. Grouping is only 
applied for the ecological assessment of rivers if they are not deemed at risk of failing good status. 

Lithuania’s  confidence  in  its  classification  of  ecological  status  is  overall  stronger  than  in  the  2nd 
RBMPs. However, for most water bodies classified in a good ecological status or potential, Lithuania’s 
confidence remains low. Confidence is to the contrary overall high for most water bodies classified in 
moderate or poor ecological status or potential. It is thus improved confidence in the classification of 
moderate or poor status rather than those in good status that caused an improvement of Lithuania’s 
overall confidence in status assessments.  

TThere has been a significant deterioration of the ecological  status of SWBs since the 2nd RBMPs 
(Figure 2). Only 36.4% of SWBs are still in good or higher ecological status, down from 51.9% in 2nd 
RBMPs. A more granular assessment shows that the ecological status by biological quality elements 
shows  an  overall  downward  trend  for  phytoplankton,  macrophytes,  phytobenthos,  and  benthic 
invertebrates while quality elements for fish are improving. Note that morphological parameters and 
thermal conditions in coastal waters are monitored but not used for status classification and many 
physico-chemical quality elements are not consistently measured across all water categories.   

Figure 3. Ecological status/potential of SWBs in 1st, 2nd, 3rd RBMPs 

Source: WISE electronic reporting 

More granular data suggest considerable differences between RBDs:  

•  Nemunas RBD: 57% of rivers and 63% of lakes not in good status  
•  Lielupe RBD: 94% of rivers and 95% of lakes not in good status 
•  Venta RBD 66% of rivers and 90% of lakes not in good status 
•  Dauguva RBD: 22% of rivers and 44% of lakes not in good status.  

13 

 
 
It is of particular concern that Lithuania’s second largest and most Northern RBD, the Lielupe RBD, 
fails to achieve good status for almost all of its 129 river and 20 lake water bodies.  

Since less expert judgement has been used and the status assessment has been increasingly based 
on  newly  monitored  data,  so  this  deterioration  could  be  partly  attributed  to  better  monitoring  of 
ecological status. 

Overall,  by  2021,  63%  river  water  bodies  and  64%  of  lake  water  bodies  failed  to  reach  good 
ecological status/potential. Moreover, all of Lithuania’s transitional and coastal waters fail to achieve 
good ecological status.  

Thus, Lithuania appears far from reaching the WFD objectives for the ecological status of SWB. Yet, 
the authorities consider that by 2027, ecological status/potential is expected to improve from now 
36.1% to then 50.8%. This means that the implementation of the Programme of Measures described 
in the 3rd RBMPs is expected to only close around 14% of the gap. 

3.2 Hydromorphological changes and artificialization (HMWBs and AWBs) 

Hydromorphological characteristics of surface water bodies concern the quantity and dynamics of 
water flow, the connection of surface water bodies to groundwater bodies, continuity of rivers, as 
well as river depth, river width and their variation in structure as well as the substrate of the riverbed 
structure of the riparian zone.  

The percentage of heavily modified water bodies in Lithuania in the 3rd RBMPs stayed overall the 
same as in the 2nd RBMPs. Figure 4 shows the high level of human intervention in the Lithuanian 
water  system.  Compared  to  other  Member  States,  Lithuania  has  the  fifth  highest  percentage  of 
heavily modified water bodies8. There are almost no artificial SWBs (only 0.42%).  

Figure 4. Percentage of heavily modified and artificial water bodies per category and total 

30%

20%

10%

0%

Rivers

Lakes

Transitional

Coastal

Territorial
Waters

Total

Heavily modified

Artificial

Source: WISE reporting 

The  main  uses  of  heavily  modified  river  water  bodies  are  agricultural  land  drainage,  urban 
development, tourism, and hydropower. The RBMPs explain that HMWBs are those water bodies that 
are regularly dredged and modified for agricultural purposes. The main physical alterations of river 
water bodies are land drainage and weirs/dams/reservoirs. 

For HMWBs, Member States are bound to define and achieve a good ecological potential (GEP). It is 
the Member States’ responsibility to define at the level of each water body this “potential” based on 

8 Based on the 20 reported MSs. 

14 

 
 
 
CIS  Guidance  Documents  No.  4  and  37.  In  respect  of  this  GEP,  Lithuania  has  defined  biological 
elements, and it has compared  good ecological potential to good ecological  status of not heavily 
modified  water  bodies.  Regrettably,  the  reported  data,  13%  is  in  GEP,  64%  moderate  ecological 
potential (MEP), 19% poor ecological potential (PEP), and 5% bad ecological potential (BEP). 

3.3 Groundwater bodies - have they sufficient water – quantitative status 

Monitoring 

There  are  no  significant  changes  as  regards  monitoring,  assessment,  and  classification  of 
groundwater quantitative status compared to the 2nd RBMPs.  

It  is  noted  positively  that  90%  of  groundwater  bodies  are  monitored  for  the  quantitative  status, 
increasing from 70% in the 2nd RBMPs. The remaining 10% of the GWBs which are not monitored, 
are  classified  based  on  expert  judgement.  Classifications  with  high  confidence  are  70 %  of  the 
assessments, and for all remaining assessments (30%) confidence is medium.  It is uncertain whether 
this  represents  a  decrease  of  confidence  since  the  2nd  RBMPs9.  Groundwater  associated  surface 
waters and/or groundwater dependent ecosystems have been considered in the Nemunas RBD, but 
not in the other three RBMPs where they have not been identified. This is regrettable because the 
WFD (Annex 2 and 5) requests that the quantitative status of GWBs is always assessed taking into 
consideration  the  ecological  needs  of  sensitive  associated  aquatic  ecosystems  (GWAAs)  and 
dependent terrestrial ecosystems (GWDTEs). 

Status assessment  

Just as for the previous cycle, all 20 GWBs are considered to be in good quantitative status, (Figure 
5). However, there is a risk that Lithuania’s reporting on the quantitative status of GWBs in the RBDs 
of Venta (LT2300), Lielupe (LT3400), and Dauguva (LT4500) maybe an too optimistic since the needs 
linked to GWAAEs and GWDTEs are not taken into account. 

9 Lithuania declared that the confidence level remained the same, despite the numbers reported through WISE which 
suggests that high confidence has decreased from 100% (2nd RBMPs) to 70% (3rd RBMPs). It is unclear, therefore, if the 
confidence level was already only 70% in the 2nd RBMPs. 

15 

 
 
Figure 5. Quantitative status of groundwater bodies in 1st, 2nd and 3rd RBMP  

Source: WISE electronic reporting 

Lithuania  has  not  classified  any  groundwater  body  at  risk  of  failing  to  achieve  good  quantitative 
status  in  2027.  However,  pressures  on  GWBs  are  apparently  increasing.  For  instance,  water 
abstraction for public water supply has been identified as a significant pressure. Moreover, saline (or 
other intrusions) impact 25% groundwater bodies (i.e., 5 of 20 GWBs). This is normally a sign of over 
abstraction in the present conditions (and poor quantitative status) and requires adaptation of the 
abstractions for a sustainable management, unless the saline impact can be related to other issues10. 
It is unclear from the 3rd RBMPs reporting if there are measures planned to reduce these groundwater 
pressures since a gap analysis for groundwater is missing.  

3.4 Protected Areas (identification, monitoring, objectives and measures) 

Lithuania has several designated protected areas including areas for the protection of bathing waters 
(Bathing Water Directive), habitat or species Natura 2000 sites (Birds and Habitats Directives) and 
Drinking  Water  Safeguard  Zones.  Rivers  are  mainly  connected  to  Natura  2000  sites  while 
groundwater bodies are mainly connected to drinking water protected areas. Two coastal and two 
transitional water bodies are linked to a protected bathing water area. In Lithuania, 17.1% of land is 
covered by protected areas11, which is below the EU average of 26%. 

10 Saltwater Intrusion - an overview | ScienceDirect Topics and  Climate Change Is Making Saltwater Intrusion Worse in 
Coastal Areas | Scientific American 
11 https://biodiversity.europa.eu/countries/lithuania  

16 

 
 
 
 
 
Table 2. Number of protected areas in Lithuania (2021) 

Number of Water Bodies Associated with protected areas in 

Rivers 

Lakes 

Coastal 

Transitional  Territorial  Groundwater 

5 

8 

45 

30 

162 

Protected 
area type 

Bathing 
waters 

13 

123 

Drinking 
water 
protection 
area 

Natura 
2000  

313 

138 

5 

16 

10 

Source: WISE e-reporting 

The data provided align with the number of protected areas and there seems to be a good coverage 
of bathing waters, drinking water protected areas, and Natura 2000 sites with almost one monitoring 
site per water body associated with protected areas. 

It is noted with concern that for surface water bodies associated with protected areas, there has been 
a deterioration in the ecological status, with high status water bodies deteriorating to good status 
and good status to moderate status. That said, the ecological status of SWBs linked to protected 
areas is a few percentage points better (ca. 42%) than the one of SWBs in general (36.1%). So, this 
may lead to conclude that while the additional measures in protected areas may be stricter than in 
non-protected areas they do not seem to be sufficient to compensate for the increase in pressures, 
which would explain the deterioration that is observed. 

As regards the chemical status of SWBs linked to protected areas, the Commission had recommended 
to reduce the number of SWBs in unknown chemical status during the last cycle. Regrettably, the 
opposite has happened. For the chemical status of surface water bodies, almost all SWBs linked to 
protected areas are reported as in “unknown” chemical status.       

17 

 
 
 
 
 
 
 
Figure 6. Status of water bodies associated with protected areas by 2022.  

Source: WISE electronic reporting 

3.5 What is being done to prevent/reduce hydromorphological pressures 

The  planning  and  implementation  of  hydromorphological  measures  in  the  3rd  RBMPs  include 
measures to improve longitudinal connectivity (fish ladders, by-pass channels, fish friendly turbines 
and fish screens), as well as other measures, though clear evidence on the degree of progress was 
not found in the revised documents although they are linked to implementation deadlines. Measures 
are planned to be funded from EU and national funds and private operators in all RBDs.  

There is no clear link between the costs identified to close the gap on good ecological potential and 
specific sources of funding. Some of these measures are a continuation from the previous cycle and 
have  already  undergone  evaluation  concerning  their  cost  and  feasibility  of  implementation. 
Selections  of  hydromorphology  measures  have  been  made  based  on  various  studies  conducted. 
Measures related to hydropower and fish passes have been chosen using information derived from 
studies and analyses conducted by scientists.   

The  3rd  RBMPs  report  that  there  is  an  authorisation  and/or  permitting  regime  in  place  to  control 
physical modifications in all four RBDs, which covers changes to the riparian area of water bodies 
according to WFD Article 11(3)(i) WFD. Whether permits have been / are subject to periodic review 
remains very uncertain, though, as permits can still be granted for an unlimited time. 

Lithuania plans to redefine its permitting regime based on a new definition of ecological flows (“e-
flows”)12 based on a national methodology for e-flows which has been developed through cooperation 
with Latvia in the cross-border project “Ecoflow”. Such transboundary cooperation should be saluted. 

12 E-flows are considered within the context of the WFD as “an hydrological regime consistent with the achievement of the 
environmental objectives of the WFD in natural surface water bodies as mentioned in Article 4(1)”. Assessment of the 
hydrological regime is not only compulsory under the WFD for assigning high ecological status to SWB, but also plays an 
important role for water permits. The WFD requires that available groundwater resources exceed the long-term annual 
average rate of abstraction. To achieve this, abstraction permits for SWBs must be granted knowing the minimum flows 
of surface water bodies that connect with ground water bodies. 

18 

 
 
 
However, implementation does not appear to have started yet and information on the timeframe was 
not found.13 

3.6 What Lithuania is doing for abstractions and water scarcity 

A  concession,  authorisation,  and  /  or  permitting  regime  to  control  surface  and  groundwater 
abstractions  and impoundments is  in  place.  Furthermore,  there  is  a  register of  abstractions  from 
surface water and groundwater and a register of impoundments. Small abstractions are defined with 
certain thresholds and those under the threshold are exempted from reporting and controls.  

Regrettably permits are still issued for an unlimited period. Yet permits can be refused or reviewed 
ad  hoc  under  specific  conditions,  such  as  administrative  and  legal  breaches  or  emergency 
environmental  situations.  E-flows  have  not  been  implemented  in  the  country,  which  implies  that 
reviews of permits lack a benchmark against which to verify if water abstractions negatively affect 
the  ecological  status  of  surface  water  bodies.  There  are  plans  to  fully  define  and  implement 
ecological flows by 2027 (see above, section 3.2 hydromorphological changes). At international level, 
it seems there is no transboundary coordination specifically on water abstraction and scarcity issues 
with neighbouring countries. 

There  are  no  basic  measures  mapped  to  reduce  pressures  on  groundwater.  Even  though  all 
groundwater bodies are in good quantitative and chemical status, basic measures are important in 
the preservation of the good status of these groundwater bodies. Examples of basic measures include 
the control of groundwater abstraction and discharges. 

3.7 Adaptation to climate change 

Climate change in the second FHRMs 

As regards flood risks, no changes were identified since the first FHRMs.14 While the second FRMP 
and the National Water Sector Plan refer to Lithuania’s policy documents for climate adaptation, they 
do  not  discuss  climate  change  issues  in  depth.  The  FRMP  provides  a  brief  overview  of  projected 
climate change impacts on the hydrological regime and flooding (both short-term and long-term), 
noting  that  recent  studies  do  not  change  previous  assessments.  The  brief  descriptions  of  climate 
trends  are presented in  the  FRMP, however,  neither  the  FRMP  nor  the  National  Sector  Water  Plan 
include  references  to  specific  research.  Additionally,  no  climate  change  scenarios  are  cited  or 
described. The three planning documents do not refer to specific measures to address climate change, 
nor do they mention climate change within their measures or as a justification for specific measures. 
For  example, for the measure  to  develop  the third PFRA,  FHRMs  and  FRMP in  the  National  Water 
Sector Plan, it is not specified whether further climate change studies or modelling would be carried 
to support this work. Some measures – for example, those for nature-based solutions – may support 
adaptation to climate change, but this is not specified in their descriptions.  

13 See Annex II, section 2.1.2 definition of quantitative status. 
14 At the time of the first FHRMs, the results of assessment of climate change suggested that spring floods will start 
earlier and the maximum discharge and intensity will show a decreasing trend. At the end of the 21st century, autumn 
and spring floods will almost merge and form a winter flood. It is expected that the frequency of hurricane storms and of 
storm water floods will increase. The water level in the Baltic Sea (Klaipeda Straight) has increased by 14.7 cm since 
1898. At the end of the 21st century, the average water level of the Baltic Sea may increase by 100 cm, and in the 
Curonian Lagoon the average water level is expected to increase by 27-63 cm. 

19 

 
 
In  regards  of  drought  risks  and  water  scarcity,  Lithuania’s  3rd  RBMPs  does  not  seem  to  include 
specific  climate  related  action  points  in  the  Programmes  of  Measures  (PoMs).  While  Lithuania 
produced  a  series  of  background  documents  outlining  the  ongoing  impacts  of  climate  change  on 
water bodies, little progress has been made in integrating the findings of these reports in the 3rd 
RBMPs and their PoMs. No information could be found in the RBMPs showing that climate change 
predictions had influenced the design of the measures.  It rather appears that evaluation of climate 
change  impacts  remains  focused  on  agriculture.  There  is  limited information  in  the  3rd  RBMPs  on 
climate change related pressures on river basins and no specific climate change adaptation measures 
could be identified in the RBMPs.  

A  report  by  the  Lithuanian  Environmental  Protection  Agency15  projects 
increased  water 
temperatures16, insufficient groundwater recharge (due to lower snow melt waters), changes in water 
quality  and  increased  concentrations  of  nitrogen  and  phosphorus.  Another  study17  found  that 
absolute nitrogen loads across all river basins are projected to increase. Yet another study18 outlines 
that  the  effectiveness  of  measures  in  the  agricultural  sector  to  reduce  nutrient  pollution  will  be 
impacted by climate change.  

In conclusion, it seems that Lithuania has conducted some research on the impact of climate change 
of relevance to water management. However, the 3rd RBMPs do not more comprehensively build on 
these findings to define measures and/or to future-proof planned measures.  

4. Policy elements contributing to zero pollution 

4.1 Surface Water: what is their chemical status 

Monitoring  

Lithuania’s monitoring network remains very insufficient as Lithuania reported an extraordinarily high 
number of surface water bodies in “unknown chemical status” (94.6%) due to the limited density of 
sites for monitoring the chemical status of surface water bodies19.  

Table  3  shows  the  chemical  monitoring  coverage  (length/area)  for  rivers,  lakes,  coastal  bodies, 
transitional bodies, and territorial water bodies. Surveillance monitoring is only in place for 8.4% and 
operational monitoring for only 5.2% of the river lengths. The level of monitoring is even worse for 
lakes (6% and 0.2% respectively). It was argued that the monitoring of lakes was very limited as it 
was  considered  that  the  risk  of  chemical  pollution  was  not  present  or  minimal.    For  coastal, 
transitional,  and  territorial  water  bodies,  Lithuania  conducts  only  operational  monitoring  but  no 
surveillance monitoring.  

It is regrettable that only few stretches of rivers are subject to monitoring at all, and that surveillance 
monitoring is completely absent for some categories of SWBs.  

15 ‘Assessment of the impact of climate change on water bodes in Lithuania based on the latest scientific works and 
research’, available at: https://vanduo.old.gamta.lt/files/Klimato_kaita.html    
16 Even though the Environmental Protection Agency expects increased water temperature, Lithuania did not report 
thermal conditions as physico-chemical QE for all surface water body types.  
17 ‘Impact of climate change on Lithuanian surface water bodies’, available at: https://vanduo.old.gamta.lt/files/report.html  
18 ‘Assessment of options for measures to reduce pollution from agricultural sources in the perspective of climate 
change’, available at: https://vanduo.old.gamta.lt/files/report1627991771354.html  
19 Lithuania declared: the chemical status was assessed according to the monitoring results, except for certain 
transboundary water bodies, where the chemical status was assessed according to the assessment made by 
neighbouring countries. 

20 

 
 
Table 3. Percentage (of length/area) included in chemical monitoring (2021) 

Chemical status monitoring 

3rd RBMPs 

River length % 

Surveillance monitoring 

River length % 

Operational monitoring 

Lake area % 

Surveillance monitoring 

Lake area % 

Operational monitoring 

Coastal area % 

Surveillance monitoring 

Coastal area % 

Operational monitoring 

Transitional area % 

Surveillance monitoring 

Transitional area % 

Operational monitoring 

Territorial area % 

Surveillance monitoring 

Territorial area % 

Operational monitoring 

Source: WISE electronic reporting 

8.4% 

5.2% 

6.0% 

0.2% 

0.0% 

100.0% 

0.0% 

100.0% 

0.0% 

100.0% 

The Commission had already flagged the need to improve monitoring previously in the 2nd RBMPs, 
calling  upon  Lithuania  “to  improve  its  monitoring  of  surface  water,  and  especially  coastal  and 
transitional  waters,  to  ensure  that  all  relevant  quality  elements  in  all  water  categories  both  in 
surveillance  and  operational  monitoring  are  covered.”  However,  in  practice,  the  coverage  of 
Lithuania’s monitoring network did not improve much. It must be noted that for the Dauguva RBD, 
Lithuania derives status assessment completely from neighbouring countries without doing its own 
monitoring as well20. 

Lithuania  has  transposed  the  EQS  Directive  and  has  incorporated  all  45  priority  substances  into 
national  legislation.  However,  the  frequency  of  Lithuania’s  monitoring  varies  between  monthly, 
quarterly, or annual intervals while the Water Framework Directive requires as minimum interval a 
monthly  monitoring.  On  the  positive  side,  monitoring  in  biota  and  sediment  is  undertaken  for  a 
majority of substances if surveillance monitoring takes place.  

While for the 2nd RBMPs the confidence was mostly low (>95%), the confidence in 3rd RBMPs is now 
largely unknown (>90%). For the remainder, the confidence level was a mixture of high, medium, and 
low level.  

Status assessment 

20 Lithuania declared: the risk of chemical pollution was not identified or assessed as minimal, including lakes, in the 
Dauguva RBD, so monitoring is not carried out here for the time being. The chemical status in Dauguva RBD was assessed 
according to the assessment made by neighbouring countries. 

21 

 
 
In  contrast  to  the  2nd  RBMP,  94.6%  of  the  surface  water  bodies  are  now  considered  in  “unknown 
status”21, 5.1% in poor chemical status and less than 1% (0.3%) in good chemical status (Figure 8).  

In the past, in the 1st and 2nd RBMPs, Lithuania reverted to grouping and extrapolations to assume 
that almost 100% of Lithuania’s surface water bodies were in good chemical status. Now, Lithuania 
reports that the chemical status has largely become “unknown”. There is no explanation given on why 
this methodology changed. 

Figure 7. Chemical status for surface water bodies in 1st, 2nd and 3rd RBMP  

Source: WISE electronic reporting 

It is of great concern that all (100%) coastal and transitional water bodies are reported to be in a 
poor status. Also, for rivers and lakes, the status is almost entirely unknown, most likely due to the 
extraordinarily low density and coverage of Lithuania’s surveillance monitoring network (coastal and 
transitional water bodies have 100% monitoring) and the absence of expert judgement and grouping 
methods.  

Where monitoring is in place, the majority of water bodies fail to achieve good chemical status due 
to the presence of ubiquitous Persistent Bioaccumulative and Toxic  substances (uPBTs) (Figure 9 and 
Figure 10). This is the case in the Venta, Lielupe and Dauguva RBD. For the Nemunas RBD, the failure 
to achieve good status is due to DEHP (phthalates used as plasticisers, which are not considered 
uPBT) which causes failure to achieve good chemical status in 5 out of the 14 water bodies where 
monitoring was undertaken and cybutryne in two water bodies. Even if uPBT substances were not to 
be taken into account, only 5% of the surface water bodies would be in good status and 1% would 
fail to achieve good status, due to DEHP in the Nemunas RBD.  

21 Determining the justification of this extraordinary high number is difficult. Lithuania did not comment or response on 
this data. However, looking at the RBMPs, there is contradictory information and data which uses non-standard 
terminology. E.g., the Venta RBMP states that no monitoring for chemical status in lakes took place, and then later the 
RBMP provides statements about monitoring chemicals in lakes. 

22 

 
 
Figure  8.  The  top-ten  Priority  Substances  causing  failure  to  achieve  good  chemical  status  including 
substances 1-33. 

Figure  9.  The  top-ten  Priority  Substances  causing  failure  to  achieve  good  chemical  status  including 
substances 1-4522. 

Source: WISE electronic reporting 

Unsurprisingly, Lithuania expects that by 2027, 0.6% of the surface water bodies will be in good 
status, while the other 99.4% will fail to reach good chemical status. 

In  terms  of  progress  with  closing  the  gap,  it  is  welcome  that  Lithuania  followed  up  on  the 
Commission’s recommendation to include in its inventories of pollution loads also aspects of diffuse 
emissions.  The  3rd  RBMPs  now  contain  sections  on  diffuse  emissions,  including  GIS  mapping  and 
details  of  the potential  risks  and  impacts  associated  with  diffuse emissions  from  agriculture  and 
atmospheric  deposition.  Regrettably,  though,  information  about  the  amounts  of  hazardous 
substances released into the water environment and their sources remains insufficient. The specific 
sources  of  pollution  hampering  the  good  chemical  status  of  waterbodies  remain  unidentified  and 
Lithuania failed to compile a complete inventory of pollution loads for priority substances. 

22 Directive 2008/105/EC as amended by Directive 2013/39/EU added 12 new substances i.e. numbered 34 to 45 to the 
priority substance list. For the 3rd RBMP, Member States have only had the obligation to monitor them. Compliance with 
the Environmental Quality Standard values for these 12 new priority substances will be assessed in 2027. 

23 

 
 
 
 
 
Furthermore, it is important to note that Lithuania did not replace expert judgement and grouping 
with actual monitored data. Instead, no assessment, unfortunately, has been made for 94.6% of the 
SWBs  at  all.  This  does  not  appear  to  be  compatible  with  requirements  of  the  Water  Framework 
Directive.  

In conclusion, the spatial and temporal scale of monitoring is insufficient to characterise the chemical 
status  of  surface  water  bodies  in  Lithuania  according  to  the  WFD.  To  close  the  gap,  surveillance 
monitoring must be established at the requisite density and depth of parameters observed. It is to 
be regretted that Lithuania did not follow up on the earlier Commission’s recommendation and thus 
without  appropriate  data  from  surveillance  monitoring,  Lithuania  reports  94%  of  SWBs  being  in 
“unknown” status. 

4.2 Groundwater Bodies: what is their chemical status 

Monitoring 

All substances causing risk of deterioration in chemical status (i.e. GWD Annex I and Annex II (Part B) 
substances  and  WFD  Annex  V  (Point  2.4.2)  core  parameters)  are  subject  to  monitoring.23  It  is 
welcomed that all 20 GWBs (100% of GWBs) are subject to surveillance monitoring, compared to 
90% in the 2nd RBMPs. However, the number of monitoring sites subject to surveillance monitoring is 
now 189, decreasing from 278 in the 2nd RBMPs. Potentially, the decrease in monitoring density has 
driven  the  decrease  in  confidence  level.  Indeed,  Lithuania’s  confidence  in  its  assessment  of  the 
chemical  status  of  groundwater  bodies  has  decreased  in  the  3rd  RBMPs.  Classification  with  high 
confidence amounts to 70.0 % of the assessments, decreasing from 100.0 % in the 2nd RBMPs. For 
the remaining assessments, the confidence is medium.  

Status Assessment 

Just as in previous cycles, all 20 groundwater bodies are considered to be in good chemical status in 
the  3rd  RBMPs  (Figure  11).  Moreover,  no  groundwater  body  is  at  risk  of  failing  to  achieve  good 
chemical  status  by  2027.  However,  the  pressures  are  increasing,  as  seen  in  Chapter  2.2  and  the 
RBMPs mention that groundwater chemical status may be affected in the future by pollution from 
fertilisers and pesticides and metabolites. There are no measures planned to reduce the pressures 
on GWBs. 

24 

 
 
 
Figure 10. Chemical status for groundwater bodies in 1st, 2nd and 3rd RBMP  

Source: WISE electronic reporting  

4.3 What Lithuania is doing to combat pollution from agriculture 

Nutrient  pollution  is  a  pressure  on  ca.  40%  of  surface  water  bodies  Lithuania  as  performed  a 
thorough gap assessment for nutrients which includes an estimate of the necessary load reduction 
for each surface water body. The gap assessment shows that the nutrient loads need to be reduced 
for 33% of surface water bodies and the load of phosphorous needs to be reduced for 10% of water 
bodies.  Lithuania’s  gap  for  nutrients  appears  significant.  According  to  the  3rd  RBMP,  it  concerns  a 
surface of 50.038 km224￼.   

Lithuania’s measures to reduce nutrient loads from agriculture include requirements for manure pits 
and  slurry  collectors,  a  prohibition  to  use  fertiliser  outside  certain  periods,  requirements  to  use 
balanced  fertilisation  based  on  fertilisation  plans,  prohibitions  to  apply  slurry  or  liquid  manure  in 
protection zones of SWBs, and in particular quantitative caps on using nitrogen and phosphorus per 
hectare of soil per year. Lithuania has addressed the recommendation of the 2nd RBMPs to improve 
the manure management by describing funding of measures and improving management of mineral 
fertiliser. However, the recommendations on additional control (enforcement) do not seem to have 
been followed. 

Lithuania included  descriptions  of measures  taken  under  the  Nitrates  Directive  in the  RBMPs  and 
assessed how different measures will contribute to the reduction of nutrient loads. For some of the 
RBDs, there is an assessment of expected impacts of the measures. This assessment suggests that 
not all water bodies where nutrient loads are risk factors will achieve good ecological status by 2027. 
Thus,  the  recommendation  of  the  2nd  RBMPs  to  provide  information  on  the  measures  under  the 
Nitrates Directives, has been fulfilled. However, the measures are likely not enough to achieve good 
ecological  status  for  all  water  bodies.  One  noteworthy  problem  in  Lithuania  seems  that  rules  on 

24 Measure P2-2.  

25 

 
 
 
manure and slurry treatment are not being complied with sufficiently by farmers. Indeed, according 
to the Dauguva RBD baseline scenario assessment, inspections related to the Nitrates Directive found 
16% to 31% non-compliance in the period from 2016 to 201925. Such high numbers of breaches are 
a reason of concern and should be considered for Lithuania’s Programme of Measures under the 3rd 
RBMPs in all RBDs. 

As regards pesticides, regrettably, no comparable gap analysis (load reductions needed to achieve 
good status) exists. The RBMPs include only basic measures to address the issue of pesticides. In the 
assessment  of pesticides based  on  groundwater monitoring,  only  a few  cases  of  exceedance  are 
observed. The surface of organic farming in Lithuania also  accounts for approximately 8% of total 
utilised agricultural land26, well below the EU-target  of 25% by 2030. In the CAP SP 2023-2027 
Lithuania reserves budget and measures to support the maintenance and new conversion to organic 
agriculture to reach 13% of the agricultural land. More organic farming will allow Lithuania to reduce 
agricultural pressures on ground and surface waters by reducing the use of pesticides and mineral 
fertilisers. 

To close the gaps for phosphorous and nitrates , the RBMPs rely both on mandatory and voluntary 
measures. The mandatory measures are set by law and most of the voluntary come as eco-schemes 
in the national agricultural strategic plan.  

Also, the RBMPs contain the basic measures and the supplementary measures funded by the CAP 
and that are part of the CAP strategic plan. There are also assessments made on how these measures 
will deliver in terms of water bodies achieving good ecological status.   

There is information on the planned measures and the funding sources are described for all of them. 
This includes basic and supplementary measures. This means that the recommendation of the 2nd 
RBMPs is fulfilled. However, from the 3rd RBMPs it is not clear how far previous measures under the 
1st and 2nd RBMPs have achieved progress, and how planned measures will reduce loads to close the 
gap. 

4.4 What Lithuania is doing to combat pollution from other sectors 

Information on drivers causing chemical pollution is not provided for Dauguva RBD (see above on the 
absence of surveillance monitoring, section 4.2). For the other three RBDs, drivers causing chemical 
pollution are given, but the relationship between measures and drivers of pollution could not be found 
and it is difficult to ascertain which measure links to a specific pressure.  

Measures have been reported for all RBDs in Lithuania. Basic measures related to water efficiency, 
including for irrigation, industry, energy and households were not implemented in the previous cycles, 
and no such measures are planned for the 2021-2027 period either. For chemical pollution, there are 
measures to improve the control of discharges with permits and to revise permits if needed. There 
are  also  measures  to  improve  the  knowledge  on  emissions  of  chemical  substances  as  well  as 
measures on information campaigns on the use and potential emissions of hazardous substances. 
The information is not detailed, and it cannot be assessed whether all relevant hazardous substances 
(priority substances and the RB specific substances) are covered by appropriate measures. There is 
limited information on the expected impacts of the planned measures.  

25 https://aaa.lrv.lt/uploads/aaa/documents/files/Dauguvos%20UBR%20bazinis%20scenarijus(2).docx  
26 Developments in organic farming - Statistics Explained (europa.eu). 

26 

 
 
More specifically in relation to industrial waste waters, currently, 99% of Lithuania’s sewage is treated 
in line with EU legislation27 in particular with the Urban Waste Water Treatment Directive. According 
to the Lithuanian Environmental Protection Agency urban wastewater treatment plants would need 
to additionally reduce by 5% nitrogen and 31% phosphorus loads28.  Lithuania reported the following 
types of measures: industrial waste water release must no longer be located close to specific water 
bodies (to be implemented no later than 2025); carry out an inventory of the wastewater discharges 
which are not registered in the integrated pollution prevention and control permits, ensure that waste 
water is not discharged into lakes; review the  Integrated Pollution Prevention and Control Permits 
and  Pollution  Permits  for  economic  entities  where  high  concentrations  of  pollutants  have  been 
identified in the discharged wastewater; review pollution permits, after the reconstruction of sewage 
treatment plants and/or the expansion of sewage networks and to specify the concentrations and 
quantities of discharged sewage in the permits, taking into account the water protection goals set 
for water bodies. Moreover, to prevent wastewater pollution from storm overflows, Lithuania foresees 
measures for 13 water bodies. The 3rd RBMP, however, provides rather limited information on the 
expected impacts of these planned measures, and their funding. 

4.5 What Lithuania is doing to combat significant pressures – overall 

assessment of the Programmes of Measures 

In the electronic reporting, Lithuania has mapped supplementary measures against KTMs in all four 
RBDs. Lithuania has mapped a total of 157 national supplementary measures against 12 predefined 
KTMs and 12 nationally defined KTMs.  The application of supplementary measures varies between 
RBDs. 

Lithuania’s  3rd  RBMP’s  Programme  of  Measures  2022-2027  suggests  that  a  prioritisation  of 
measures in the RBMPs has taken place based on a cost-effectiveness analysis. Reducing sources of 
diffuse pollution ranks highest and is tackled through a regulation of fertilisers to reduce leaching of 
phosphorus and nitrogen into surface and ground water bodies.  

5. Exemptions and economics 

5.1 To what extent are exemptions applied in Lithuania 

It is important to note that Lithuania has invoked in the 3rd RBMPs the exemptions of Article 4(4) 
(time related exemptions to delay deadlines) for all water bodies that are not in good status. On the 
other hand, Lithuania has not invoked exemptions to lower the environmental objectives under Article 
4(5) WFD. The exemptions under Article 4(4) were applied based on: 

•  Technical unfeasibility in 747 SWBs (62.6 %) for ecological status/potential and in 12 SWBs 

(1 %) for chemical status. 

•  Natural conditions in 473 SWBs (39.6 %) for ecological status/potential and in 60 SWBs (5 

%) for chemical status. 

There are some changes, however, as to how the exemptions of Article 4 (4) WFD were invoked in 
this third cycle. In the 2nd RBMPs, the exemptions were still applied as follows: 

27 https://water.europa.eu/freshwater/countries/uwwt/lithuania  
28 Detail data can be found in infographics, tables and maps: 
https://vanduo.old.gamta.lt/files/ataskaita.html#rezultatų-santrauka.  

27 

 
 
•  Technical feasibility in 565 SWBs (47.7 %) for ecological status/potential and in 12 SWBs 

(1 %) for chemical status. 

•  Natural conditions in 145 SWBs (12.2 %) for ecological status/potential. 

It can be concluded that in the 3rd RBMPs, the exemptions under Article 4 (4) WFD have been invoked 
more often on grounds of “technical feasibility” to achieve good ecological status and more often also 
on grounds of “natural conditions” than before.  

It is also noted that, differently from the 2nd RBMPs, for chemical status and for the few SWBs where 
the status is unknown, Lithuania has used exemptions pursuant to Article 4(4) on grounds of natural 
conditions. It is worth recalling, that the same water body can be subject to several exemptions, which 
makes a direct comparison difficult.  

Figure 11. Exemptions applied to Lithuania’s water bodies in the 3rd RBMPs. 

Source: WISE electronic reporting 

Justifications  for  the  use  of  exemptions  have  been  provided  at  the  water  body  level  in  annexes. 
However, the justifications are only briefly explained and are generic meaning that they are repeated 
over many water bodies.  

No exemptions according to WFD Article 4(5), Article 4(6), Article 4(7) of the WFD and Article 6(3) of 
the Groundwater Directive have been applied in the 3rd RBMPs. 

It  should  be  noted,  though,  that  Lithuania  cannot  invoke  the  exemption  of  Article  4  (4)  WFD  for 
reasons other than natural conditions after 22/12/2027, because Article 4 (4) (c) WFD foresees that 
time extensions shall be limited to a maximum of two further updates of the river basin management 
plan except in cases where the natural conditions are such that the objectives cannot be achieved 
within this  period.  The term  'natural  conditions'  refers  to  the  conditions  which  dictate the  rate  of 
natural recovery. It recognises that it may take time for the conditions necessary to support good 
ecological status to be restored and for the plants and animals to recolonise and become established. 
This must be demonstrated at the level of each water body. 

28 

 
 
5.2 Use of economic analysis and water pricing – cost recovery 

Lithuania presents a detailed economic analysis in a supporting document to the 3rd RBMPs. For all 
4  River  Basin  Districts,  there  are  long-term  forecasts  of  water  supply  and  demand  which  are 
differentiated over type of supply sources and user types / sectors; volume, costs and price estimates 
associated  with  the  various  water  services,  all  differentiated  over  the  broad  water  user  sectors 
(agriculture,  industry  and  households);  as  well  as  estimates  and  forecasts  of  the  relevant 
investments. The RBMPs appear not fully rigorous in distinguishing the concepts water services, water 
uses and water user sectors.  

The RBMPs do not present a clear cost-effectiveness analysis (CEA) that has informed the selection 
of measures to be included in the Program of Measures. However, Lithuania’s National Water Sector 
2022-2027 action plan talks about ‘performing a cost-effectiveness analysis’ by comparing costs of 
alternative options to achieve a good status. Yet, the scope of this analysis remains unclear because 
there are hardly any references to background documents on the CEA carried out.  

The economic analysis gives a detailed account of the water pricing policies, many aspects of which 
contribute to providing adequate incentives for an efficient water use. The water abstraction permit’s 
fee  as  well  as  drinking  water  tariffs  have  a  volumetric  component;  the  unit  rate  increases  over 
consecutive consumption volume brackets; the water bill for water services provides a transparent 
specification of the various price components; and prices vary across regions differing in cost and 
water status profile. However, irrigation water is charged with a flat rate, probably per hectare of 
arable land, and in all RBDs there are some specific water services provided well below the cost price, 
justified by a specification of the economic, social and environmental effects of using prices conform 
full cost recovery. The design of the water pricing policies is informed by empirical price elasticities.  

The RBMPs provide overall cost recovery figures for collective water supply services, namely water 
supply  and  sanitation  services  combined  and  for  each  service  separately.  The  account  of  the 
calculations of the cost recovery rate present figures on costs and revenues in a transparent manner, 
also reporting on subsidies. For water supply services as a whole, the RBMPs compare prices implied 
by (nearly) full cost recovery in a so-called “current scenario” and cost-recovery levels in a “potential 
scenario” where investment costs covered by EU grants are considered as depreciation costs. On this 
basis, the choice has been made to set prices conform the “current scenario;” the reported calculations 
indicate that this still results in recovering most of the water services’ costs, with the exception of 
the Dauguvo RBD (about 40% rather than about 85% cost recovery).  

While the background documents report on the revenues obtained from the broad water user sectors 
and also on subsidies, the RBMP’s appear to lack a clear statement on the overall adequacy of their 
contributions to the water services’ costs as well as the application of the polluter-pays-principle.  

The economic analysis also reports on the appraisals of the environmental costs and how they have 
informed  water  prices  and  other  pricing  policies.  For  the  water  user  sectors  agriculture  and 
hydropower,  two  methods  have  been  used:  the  tax  rate  on  nitrogen  emissions  and  on  natural 
resources  respectively  have  been  used  to  appraise  these  sector’s  environmental  costs  (benefit 
method),  supplemented  by  the  costs  of the  other measures  to  achieve  good  status to the  extent 
incurred by these sectors (cost-based method). For the other sectors, namely the collective water 
services (hence households), industry and aquaculture, only the benefit method has been used.  

Note that this assessment is based on the stringent assumption that the unit rates adequately reflect 
the costs of the actual pollution and that these taxes are levied on the actual polluters rather than 
users. However, the RBMP assessment recognises that for important pollution pressures, this is not 

29 

 
the case. For industrial wastewater, the rate if pollution fees do not reflect the ensuing environmental 
damage while hazardous substances released by industry are often insufficiently accounted for and 
therefore the related damage is not compensated in any way through the cost recovery mechanism. 
Both cases indicate that further improvements in the application of the polluter-pays-principle are 
possible.    

6. WFD recommendations 

Recommendations - Lithuania should: 

1.  accelerate action and enhance the overall level of ambition for restoring to good ecological status (natural 
water bodies) or good ecological potential (heavily modified water bodies) and good chemical status of 
surface  bodies  to  reduce  the  compliance  gap  as  much  as  possible  by  2027.  This  presupposes  that 
Lithuania: 

2.  addresses the density of its entire monitoring network for surface water bodies as a matter of urgency. 
Despite  Lithuania’s  overall  progress  on  other  aspects,  the  spatial  and  temporal  scale  of  Lithuania’s 
monitoring network remains by far insufficient to provide reliable information on the chemical status of 
surface water bodies in line with Annex II, Section 1.3 WFD. This shortcoming already existed in the 1st 
and 2nd RBMPs and has not been addressed so far contrary to preceding Commission recommendations. 
Lithuania’s monitoring network should be upgraded speedily to fully meet the requirements of Article 8 so 
that the network can provides a coherent and comprehensive overview of the chemical and ecological 
status within each river basin district and permits a reliable classifications of water bodies. 

3.  adopts  more specific  and more  targeted  measures  to  reduce  the  pollution  of  its  surface water  bodies 
regarding nitrogen and phosphorus from intensive agricultural activities to reduce pressures. Furthermore, 
Lithuania should more regularly review the effectiveness of the existing and future measures to reduce 
pressures from diffuse agricultural pollution to establish a feedback loop between measures taken and 
impacts achieved to allow for continuous improvements;  

4.  accelerates measures to improve wastewater treatment in particular by  connecting  septic and sewage 

storage tanks in lower populated areas with wastewater treatment facilities. 

5.  maps more effectively measures to improve the ecological status of coastal and transitional water bodies, 

including measures to reduce nitrate and nitrogen pollution. 

6.  Regarding the use of economic tools, funding and cost-recovery for water services, Lithuania should: 

7. 

provide more detailed information on the prioritisation of the measures together with a judgement on the 
most cost-effective combination of measures. Lithuania should explore in more depth how polluters can 
be made to pay for cleaning up chemical and ecological pollution of surface water bodies, in particular for 
industrial wastewater discharges.  

a.  make polluters pay for cleaning up pollution by covering costs of waste-water treatment plants such 

that good chemical status of surface water bodies can be achieved.  

8.  Regarding additional measures to reduce the existing environmental challenges and pressures, Lithuania 

should: 

9.  adopt  time-bound  measures  and  earmark  sufficient  resources  to  identify  and  sanction  breaches  of 
compulsory rules constraining the use of mineral fertilisers, slurry and manure in all RBDs. Lithuania should 

30 

 
ensure regular inspections to ensure that the sector complies with requirements under the WFD and the 
Nitrates Directive for manure and slurry treatment;    

10.  assesses comprehensively and implement alternatives to intensive agriculture and uses eco schemes to 
promote organic farming (which is still below EU average) in regions where pressures on the ecological 
status of surface water (and the chemical status of ground water bodies) are high;  

11.  link  measures  to  reduce  pollution  from  industry,  transportation,  and  the  urban  sector  more  clearly  to 

pressures and quantify more precisely the gap;  

12.  accelerate the revisions of permits and ensure that these permits are periodically reviewed as required by 
the law and upgrade urban and industrial wastewater discharges and reduces chemical pollution from 
urban run-off. 

13.  accelerate the recovery periods by reducing pressures and taking action at the level of each water body by 

reducing pressures and cleaning up pollution; 

14.  use  all  programmed  amounts  for  sustainable  water  management  and  climate  adaptation  under  the 

Cohesion Policy 2012-27. 

15.  As regards adaptation to climate change and water scarcity, Lithuania should: 

16.  make permits for abstractions from surface water bodies dependent on the respect of ecological flows 

based on an agreed and binding methodology to calculate ecological flows.  

17.  timely limit water abstraction permits because unlimited permits hamper are difficult to reconcile with the 

obligation to ensure periodic reviews of abstraction controls (Article 11(3)(e) and 11(3)(g) WFD).  

a.  For  the  five  GWBs  in  the  Lielupe  and  Nemunas  RBDs  which  are  under  significant  pressures  from 
abstractions for public water supply, it is recommended to adopt measures for enhancing efficiency 
and reducing water consumption per capita to prevent that the five groundwater bodies run the risk of 
failing good quantitative status in the future.  

b.  map basic measures to groundwater pressures to preserve the good quantitative and chemical status 

of its groundwater bodies. 

18.  should establish more explicit links between, on the one hand, the national climate adaptation strategy, 
and related background documents on climate change impacts, and the RBMPs and its Programme of 
Measures, on the other hand;  

19.  Regarding transboundary cooperation, Lithuania should: 

a. 

continue its effort on transboundary cooperation to increase comparability on reference conditions, 
monitoring and classification with its neighbouring countries.  

20.  Regarding  the  use  of  exemptions,  Lithuania  should  apply  these  in  line  with  ECJ  jurisprudence  on  the 
restrictive  interpretation  of  exemptions  and  better  justify  the  use  of  exemptions,  providing  sufficiently 
detailed justifications at the level of the water body and ensure that their application is regularly reviewed. 
This implies in particular: 

a.  Recognising that the possibilities for time extensions (Article 4 (4)) are extremely limited and will no 

longer be allowed after 2027 (except if duly justified for natural conditions).  

b.  Where Lithuania intends to invoke “natural conditions” as reason for exempting surface and/or ground 
water bodies according to Article 4 (4) WFD after 2027, it will be necessary to demonstrate the recovery 
period for ecological and chemical status at the level of each individual water body failing good status 
in 2027. 

31 

 
c.  Where new projects, including dams and water transfers, are carried out, these should be made subject 
to a thorough assessment of the impact on water bodies, in accordance with Art 4(7), and where so 
required  because  potential deterioration  of  status /potential  may  occur,  a  thorough  justification  by 
detailing cumulative effects, the assessment of better environmental options, and the measures taken 
to mitigate the adverse impacts of new developments.  

21.  Regarding the classification, monitoring and assessment problems, Lithuania should: 

22.  consider GWAAEs and GWDTEs in the establishment of threshold values (and establishing the quantitative 
status of GWBs) in all RBD; consider saline or other intrusions in the establishment of threshold values in 
all RBDs (not only in Nemunas RBD - LT1100); coordinate threshold values with neighbouring countries.  

a. 

b. 

c. 

further improve monitoring to increase confidence in the classification of ecological status of surface 
water bodies where good status / potential is made with low confidence and where expert judgment is 
used instead of data (as the Commission already recommended in the assessment of the 2nd RBMPs)  

further improve the monitoring of the quantitative status of GWBs so that confidence increases overall, 
considering that 30% of GWBs are still assessed with medium confidence and that 10% of all GWBs 
are not quantitatively monitored.  

include specifically for surveillance monitoring sufficiently representative number and types of SWBs 
in its surveillance monitoring program to provide a reliable assessment of the overall surface water 
status within each catchment and sub-catchment of the river basin district.  

d.  make  a  precise  gap  analysis  (load  reductions  needed  to  achieve  good  status)  for  pesticides;  and 
commit funding for concrete and specific measures to reduce pressures form pesticides in surface and 
groundwater water bodies.  

e.  adopt more measures to improve the poor chemical status of Lithuania’s coastal, transitional, and 
territorial  water  bodies,  based  on  a  source-to-sea-approach  that  also  identifies  origins  of  coastal 
pollution inland. 

f. 

include all QEs in assessing the ecological status for all surface water bodies, in particular, improve 
the  monitoring  of  RBSPs  in  rivers  and  lakes  and  hydromorphological  and  physico-chemical  QEs  in 
coastal and transitional waters. 

g.  monitor and contain invasive alien species and in particular adopt measures to constrain the spreading 

of American crayfish. 

h. 

i. 

foresee sufficient funding to achieve a good ecological potential for each heavily modified water body.  

implement ecological  flows  and  make  water  permits  for  abstractions  dependent  on  the  respect  of 
ecological flows.  

23.  consider the GWAAEs (groundwater associated aquatic ecosystems) and GWDTEs (groundwater dependent 
terrestrial ecosystems) for assessing the quantitative status of GWBs in all four river basin districts and 
ensure designated protected areas are afforded adequate objectives and measures for their protection.  

j. 

should  (continue  to)  accurately  quantify  nitrate-,  nitrogen-,  phosphorus-  and  phosphate  loads  per 
sector in the RBMPs gap analysis for calibrating its programme of measures.  

k.  Very  considerably  improve  monitoring  such  that  its  confidence  in  the  results  of  chemical  status 
assessments  of  groundwater  increases  to  understand  why  concentrations  of  pesticides  and  their 
metabolites  from  agriculture are  increasing  in  groundwater  bodies  and  take  effective measures  to 
reduce that pressure.  

32 

 
SECTION B: 
FLOODS DIRECTIVE 

33 

 
 
 
7. Flood risk management under floods directive (FD) 

The Directive requires each Member State (MS) to i) scan its territory for flood risks, ii) assess the 
potential adverse consequences of future floods for human health, the environment, cultural heritage 
and  economic  activity, iii)  identify  the  significant  risks,  iv)  map  the flood  extent  and  the  potential 
adverse consequences, and v) take measures to reduce the flood risk. These activities are reflected 
in  (a)  the  preliminary  flood  risk  assessments,  or  PFRAs  (including  the  identification  of  areas  of 
potential  significant  flood  risk,  or  APSFRs),  (b)  the  preparation  of  flood  hazard  and  risk  maps,  or 
FHRMs,  and  (c)  the  establishment  of  flood  risk  management  plans,  or  FRMPs.  The  preliminary 
assessments, mapping and planning for flood risk are repeated in six-yearly cycles. 

There  are  four  Units  of  Management  (UoMs)  in  Lithuania,  which  are  the  same  as  the  Water 
Framework  Directive’s  River  Basin  Districts  (RBD).  The  possible  sources  of  floods  considered  are: 
fluvial, pluvial, groundwater, sea water, and those coming from Artificial Water Bearing Infrastructure.  

Lithuania  has  designated  129  Areas  of  Potential  Significant  Flood  Risk  (APSFRs).  The  impacts  of 
climate change on flood risk have been considered in Lithuania. Indeed, for all UoMs, an analysis of 
the latest hydrometeorological data and scientific publications of Lithuanian experts was conducted 
in order to review potential climate change impacts. This analysis has confirmed the findings from 
the first cycle indicating that spring floods  tend to decrease in Lithuania while the significance of 
floods originating from rainfall events constantly grows. No new data was found which would allow 
to predict any changes in water level in the Baltic Sea and the Curonian lagoon. The report comes to 
a general conclusion that flood risk trends in all UoMs remain the same as those depicted in the first 
PFRA. 

7.1 Flood hazard and risk maps 

Lithuania  is  using  a  web  map  covering  the  whole  territory29  for  their  FHRMs.  Such  maps  were 
prepared at the national level and cover all four UoMs. The website of the EPA of Lithuania30 informs 
that  the  APSFRs  remain  the  same  as  in  the  first  cycle.  The  Lithuanian  EPA’s  webpages  on  the 
management of floods31 provide links to the PFRA and to the GIS data sets used for the FHRM, which 
show  the  APSFRs.  Maps  for  floods  with  low  probability  (1/1 000  years),  with  medium  probability 
(1/100 years) and with high probability (1/10 years) are provided. Flood extent is shown on the maps. 
The report on the Update of the Flood Hazard and Risk Maps Data32 states that depth is mapped, 
however, it is not possible to see it on the online FHRM33.. The maps show the number of inhabitants 
and the potential costs from flood damage, but not the type of economic activity. The report on the 
Update  of  the  Flood  Hazard  and  Risk  Maps  Data  states  that  all  the  data  on  economic  activities 
(potential damage costs) was updated taking into account inflation since 201334. The maps also 
show  the  industrial  installations  covered  by  the  Industrial  Emissions  Directive.  as  well  as  the 

29 https://potvyniai.aplinka.lt/ 
30 Preliminarus potvynių rizikos vertinimo atnaujinimas 2011-2018 m. (English: Update of the Preliminary Flood Risk 
Assessment 2011-2018), website of the EPA of Lithuania, 
https://vanduo.old.gamta.lt/files/Preliminary_flood_risk_assessment_2011_2018.pdf 
31 https://aaa.lrv.lt/lt/veiklos-sritys/vanduo/upes-ezerai-ir-tvenkiniai/potvyniu-rizikos-valdymas/ 
32 ibid 
33 Lithuanian subsequently clarified that depth information is only available in the data for download - 
https://potvyniai.aplinka.lt/duomenys/Potvyniu_gyliai_01_1_10proc.zip In the future, it is planned to update the public 
online map and provide more valuable information. 
34 Lithuania subsequently informed that type of economic activity is only available in downloadable FHRM layer sets 
https://potvyniai.aplinka.lt/duomenys/Potvyniu_rizikos_zonos_01_1_10proc.zip;layer "Riz_ekon_priekrantes_text", 
"Riz_ekon_sniegoliciu_text" 

34 

 
 
potentially  affected  protected  areas  identified.  The  FHRM  background  information  is  found  in  two 
different documents – the Report on the Update of the Flood Hazard and Risk Maps Data and on the 
website of the EPA of Lithuania35. 

In terms of the way in which information about the maps is conveyed to the public, compared to the 
first FHRMs, the new maps do not hardly provide contextual information, but there are links to the 
websites of the Ministry of Environment (MoE), the EPA and documents describing the update of the 
FHRMs and related information36. 

As stated in the report, compared to the previous cycle, the methodologies used to prepare flood 
hazard maps have remained the same. However, for the second FHRMs the data related to the risk 
maps were updated, e.g. the indicative number of inhabitants affected was calculated using 2021 
population census spatial data. 

As regards the consideration of climate change effects in the preparation of flood hazard and risk 
maps, reference is made to section 3.7 on ‘adaptation to climate change’.    

7.2 Flood risk management plans 

Objectives and measures 

The FRMP, the National Water Sector Plan and the Action Plan can be downloaded from a web page37 
of  the  Environmental  Protection  Agency  of  Lithuania.  These  three  planning  documents  set  i)  one 
common objective and ii) one common task (a sort of sub-objective) for all four UoMs. The common 
objective calls for the reduction of flood risks. The common task calls for risk assessment, though 
further details are not provided. The second FRMP’s objective (and the National Water Sector Plan’s 
task) are linked to indicators, making the objective more measurable. The links to measures are now 
provided more clearly in the three planning documents.  

There has been a big effort done of streamlining. Indeed, the second FRMP has a simpler structure 
for its objective and task compared to the 17 objectives presented in the first FRMP; however, this 
has made the objective in the second FRMP (and the related task in the National Water Sector Plan) 
less specific than those in the first FRMP. The achievement of the second FRMP’s objective will be 
monitored using quantitative indicators (which are however included in the National  Water Sector 
Plan and not in the FRMP itself). These indicators are not linked to specific measures, and Lithuania’s 
three planning documents do not provide information specifically on the monitoring of measures. The 
FRMP states that flood prevention, risk management and education about threats are important for 
human  health,  economic  activity,  the  environment,  and  cultural  heritage.  Lithuania  reported  12 
measures. All three planning documents list measures (though the numbers are different across the 
three documents and different to the number of measures reported). The National Water Sector Plan 
identifies the following three groups of measures: i) strengthen flood prevention in flood risk areas; 
ii) reduce potentially flooded populated areas; and iii) prepare strategic documents for the new cycle 
of implementation of the Floods Directive. Lithuania reported all of its measures as high priority. 
None  of  the  three  planning  documents  assessed  provide  information  on  priorities  assigned  to 
measures or on methods of prioritisation. The second FRMP depicts the progress of implementation 

35 Preliminarus potvynių rizikos vertinimo atnaujinimas 2011-2018 m. (Update of the Preliminary Flood Risk Assessment 
2011-2018), website of the EPA of Lithuania, 
https://vanduo.old.gamta.lt/files/Preliminary_flood_risk_assessment_2011_2018.pdf  
36 https://aaa.lrv.lt/uploads/aaa/documents/files/Metodika_20220509.pdf  
37https://aaa.lrv.lt/lt/veiklos-sritys/vanduo/upes-ezerai-ir-tvenkiniai/potvyniu-rizikos-valdymas/potvyniu-rizikos-valdymo-
planas-2023-2027-m/    

35 

 
 
of  the  measures  taken  in  the  first  FRMP.  However,  Lithuania’s  three  planning  documents  do  not 
provide information specifically on the monitoring of measures. 

The Action Plan provides investment costs for some measures: specifically, for 41 actions that are 
structural measures. No description was found in the documents on how the investment costs were 
calculated. The National Water Sector Plan (in its annex 1) and the Action Plan (in section 3 of its 
main table) identify funding sources for each flood measure or action. The funding sources cited are: 
the  state  budget,  state  forestry  office,  EU  funds,  municipal  budgets,  and  the  owners  of  movable 
cultural heritage (this includes artworks, books and other artifacts), though for the latter source of 
funding the types of entities who hold the heritage are not specified. The National Water Sector Plan 
provides three indicators for overall benefits expected from flood risk management, but they are not 
linked  to  specific  measures.  The  FRMP  briefly  refers  to  the  use  of  cost-benefit  analysis,  without 
providing details on the methods or results. It states that coordination between the FRMP and the 
WFD was ensured, but it does not include details on how the this was done for the development of 
the second FRMP and the third RBMPs under the WFD. Yet, is briefly mentioned in the FRMP that flood 
measures do not hinder the achievement of the objectives of the WFD. 

As regards the types of measures, one of the three measure groups in the National Water Sector 
Plan is to strengthen flood prevention in flood risk areas. Lithuania reported 12 measures in total. 
Out of which:  four prevention measures, eight preparedness measures and none for protection. The 
plan states that its overall aim includes preparation for floods. The Action Plan lists four preparedness 
measures.  No  information  was  found,  however,  on  measures  for  flood  forecasts  or  early  warning 
systems.  The  FRMP  mentions  that  one  of  the  most  important  flood  prevention  measures  was 
implemented during the first cycle of the FD implementation: the Law on Special Conditions for Land 
Use was amended with restrictions for new construction in flood hazard areas. This law limits the 
construction of new, non-essential and unprotected buildings in flood hazard areas. This includes 18 
structural  actions  that  were  designated  as  the  highest  priority.  After  implementation  of  these 
measures, approximately 8 000 inhabitants38 will be protected. 

As regards progress on implementation, second FRMP reviews the implementation of measures in 
the first FRMP. It notes that many key measures set out in the first FRMP have been or were being 
completed and a few had been abandoned. Lithuania reported the progress of implementation of its 
12 measures: four preparedness measures were reported as not started; four preparedness measures 
were reported as ongoing (recurrent e.g., maintenance works); and four prevention measures were 
reported as undergoing construction. The plan explains that most of the highest priority actions from 
the  first  plan  were  implemented  or  they  would  be  under  implementation  in  202339.  Some  of  the 
difficulties  quoted  to  implement  some  measures  are:  in  some  areas,  it  became  clear  that  some 
measures may cause irreparable damage to cultural heritage, in other heavily built-up areas, there 
was not enough state land available to build structural measures, in other cases, local communities 
or  municipalities  did  not  support  a  measure.  Also,  some  measures  were  abandoned  because  a 
detailed assessment of their feasibility (also considering increases in construction costs and other 
factors) showed they were no longer cost-effective, as the potential damage avoided would be less 
than construction costs of structural measures. The FRMP does not, however, provide information on 
the number of measures affected, nor further detail on the measures not implemented. Nonetheless, 
the 41 measures in the Action Plan include the lower priority structural actions from the first FRMP 
that were not implemented but remain planned.  

38 pp.11-12. 
39 pp.11-12 

36 

 
 
Governance 

It  is  noted  very  positively  that  Information  on  the  draft  FRMP  was  submitted  to  the 
neighbouringneighbouring competent  authorities  of Latvia  and  Poland,  and  vice  versa.  Lithuania’s 
FRMP  states  that  none  of  its measures  would  increase  the  risk  of  flooding in  the  downstream  or 
upstream regions of the same river in neighbouring countries. 

The plan states that the public was able to review documents prepared for the implementation of 
the Floods Directive and provide comments. It provides brief information on the consultation for the 
draft second PFRA and the draft FHRM. While the FRMP provides the comment periods for the PFRA 
and  FHRM  consultations,  it  does  not  indicate  the  period  for  the  FRMP  consultation.  There  is  no 
information  in  the  FRMP  itself  whether  comments  from  stakeholders  were  received,  nor  is  there 
information on meetings or other direct consultations with public. 

Progress identified in the second FRMPs 

The  second  FRMP’s  objective  (and  the  National  Water  Sector  Plan’s  task)  are  linked  to  indicators, 
making them more measurable. Achievement of the second FRMP’s objective will be monitored using 
quantitative indicators (which are however included in the National Water Sector Plan and not in the 
FRMP  itself).  The  links  to  measures  are  now  provided  more  clearly.  Also,  the  second  FRMP  has  a 
simpler structure for its objective and task compared to the 17 objectives presented in the first FRMP. 
The  planning  documents  related  to the  second  FRMP  include  natural  water  retention  and  cultural 
heritage protection related measures. While the second FRMP and the National Water Sector Plan 
refer to Lithuania’s policy documents for climate adaptation (they did not previously), climate change 
issues are discussed briefly. 

As regards the consideration of climate change effects in the preparation of flood risk management 
plans, reference is made to section 3.7 on ‘adaptation to climate change’.    

8. FD recommendations 

Recommendations - Lithuania should: 

reflect in the FHRM all identified APSFRs. 

show in the FHRM the type of economic activity of the area potentially affected. 

specify in the FRMP how the FHRM was used in setting objectives and choosing measures; 

provide links in the FRMPs to the national map portal showing the FHRMs as well as summary maps of the 
APSFRs; 

ensure that the FRMP are a self-standing document, with clear links and references, where relevant, to other 
national planning documents, and vice versa; 

make an assessment of the progress made towards the achievement of the objectives in the FRMP; 

provide cost information for all measures, not just structural measures in the FRMP; 

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provide information on the methods used to prioritise measures in the FRMP; 

discuss the likely impact of climate change on flood risk in detail in the FRMP, including any updates since the 
PFRA; 

consider Insurance as a measure for adaptation to climate change; 

clearly set out in the FRMP the number of measures/actions being implemented, how they will be monitored 
and should be in agreement with the National Water Sector Plan and its Action Plan; 

where  relevant,  incorporate  CBA  for  the  prioritisation  of  measures  and  provide  a  clear  description  of  the 
methodology used in the FRMP; 

a)  provide detail on the public consultation and stakeholder involvement, such as the duration, specific 
stakeholders that participated, the meetings and advisory groups convened, the comments received, 
and how they were taken into accoun 

b)  where appropriate should consider flow velocity or relevant water flow and the FRMP flood conveyance 

routes, as these are relevant to emergency response. 

38