COMMISSION STAFF WORKING DOCUMENT Third River Basin Management Plans Second Flood Hazard and Risk Maps and Second Flood Risk Management Plans Member State: Czechia 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: Czechia, adaptation to climate change, application of EU law, environmental risk prevention, flood, risk management, water, water management, water pollution, watercourse

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  EN 

   EUROPEAN COMMISSION  Brussels, 4.2.2025  SWD(2025) 33 final  COMMISSION STAFF WORKING DOCUMENT Third River Basin Management Plans   Second Flood Hazard and Risk Maps and Second Flood Risk Management Plans Member State: Czechia              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) 28 final} - {SWD(2025) 29 final} - {SWD(2025) 30 final} - {SWD(2025) 31 final} - {SWD(2025) 32 final} - {SWD(2025) 34 final} - {SWD(2025) 35 final}  
 
 
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Country specific staff working document 

Czechia 

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  EN 

 
 
 
 
 
 
 
 
Content 

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

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

1. General info, Member State characterisation ............................................................................................................. 4 

2. Horizontal aspects ...................................................................................................................................................................... 8 

2.1 Governance ............................................................................................................................................................................ 8 

2.2 Characterization of River Basin District ................................................................................................................. 8 

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) ........................................... 18 

3.5 What is being done to prevent/reduce hydromorphological pressures ............................................ 20 

3.6 What Czechia is doing for abstractions and water scarcity .................................................................... 20 

3.7 Adaptation to climate change .................................................................................................................................. 21 

4. Policy elements contributing to zero pollution ........................................................................................................ 23 

4.1 Surface Water: what is their chemical status ................................................................................................. 23 

4.2 Groundwater Bodies: what is their chemical status .................................................................................... 25 

4.3 What Czechia is doing to combat pollution from agriculture ................................................................ 26 

4.4 What Czechia is doing to combat pollution from other sectors ........................................................... 28 

4.5  What  Czechia  is  doing  to  combat  significant  pressures  –  overall  assessment  of  the 
Programmes of Measures .................................................................................................................................................. 30 

5. Exemptions and economics ............................................................................................................................................... 30 

5.1 To what extent are exemptions applied in Czechia...................................................................................... 30 

5.2 Use of economic analysis and water pricing – cost recovery ................................................................ 31 

6. WFD recommendations ........................................................................................................................................................ 33 

SECTION B: FLOODS DIRECTIVE .................................................................................................................................................. 38 

7. Flood risk management under floods directive (FD) ............................................................................................ 39 

7.1 Flood hazard and risk maps ...................................................................................................................................... 39 

7.2 Flood risk management plans .................................................................................................................................. 40 

8. FD recommendations ............................................................................................................................................................ 42 

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SECTION A: 
WATER FRAMEWORK 
DIRECTIVE 

2 

 
 
 
1. General info, Member State characterisation

The Czech Republic (CZ) is a landlocked country, bordered by Austria to the south, Germany to the 
west, Poland to the northeast, and Slovakia to the southeast. CZ has a hilly landscape that covers an 
area of 78,871 square kilometres with a mostly temperate continental climate.  

CZ (10.8 million) has a population density of 133 per km2, which is above EU average. Bohemia, to 
the west, consists of a basin drained by the Elbe and the Vltava rivers, surrounded by mostly low 
mountains, such as the Krkonose range of the Sudetes. Moravia, the eastern part of the country, is 
drained mainly by the Morava river, and it also contains the source of the Oder River. Water from the 
Czech Republic drains to three different seas: the North Sea, the Baltic Sea and the Black Sea.  

The territory of Czechia covers three international river basin districts (RBDs): The Danube River Basin 
(CZ 1000), the Elbe River Basin (CZ 5000) and the Oder River Basin (CZ 6000). 

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.  

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By  September  2023  Czechia  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. 

The  below  table  summarises  the  key  data  on  the  pressures  on  /  the  status  of  surface  and 
groundwater bodies in the Czech Republic as per the data reported in Czechia’s 3rd RBMP and related 
electronic reporting in WISE.  

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Changes in Status, Pressures, Exemptions & Measures  

Surface 
Water 
Bodies   

Trend (% good 
status/potential) 

100%

ECOLOGICAL 
STATUS  

50%

0%

100%

18,8%

5,9%

2015 2021

70%

50%

CHEMICAL 
STATUS  

38,9%

0%

2015 2021

Main Pressures & Changes & Exemptions 

The main pressures of Czechia’s SWBs are the insufficient treatment of waste waters (affecting 74% SWB) and diffuse pollution from 
agriculture (affecting 67% SWB). Surface water bodies are impacted by nutrients (affecting 82 % of all SWBs  - up from 41% SWB in the 2nd 
RBMPs ) causing severe euthrophication of rivers and lakes. The deterioration of the ecological status from 18.8% to 5.9% since 2015 
appears mainly due to the improved surveillance monitoring (coverage increased from 8% to 13% for rivers and from 10% to 48 % for lakes) 
and stricter boundaries for physico-chemical elements (N + P). The ecolocigal status of rivers is also affected by many impoundments to the 
free flow of rivers: Less than 20% of Czechia’s rivers benefit from sufficient continuity. Czechia is in the process of developing a new 
methodology for ecological flows. Only 12.2% of SWBs are expected to reach the objective of a good ecological status by 2027. Overall, the 
improved monitoring and stricter boundaries between 2nd and 3rd RBMP have put Czechia in a better position than before to tackle the root 
causes for the massive nutrient pollution of its rivers and lakes. This challenge is very signficiant.   

Similar to the analysis of the ecological status, Czechia improved its monitoring between the 2nd and 3rd RBMP which allowed for a better 
identification of pressures on rivers and lakes. Since the 2nd RBMPs, 84% of all rivers are now being monitored, that is a significant increase 
in monitoring by +30%, and also more chemicals are being considered in the status assessment. Pressures are similar to those for the 
ecological status, namely discharges not connected to the sewerage network, pollution from agriculture (pesticides) well as insufficienty 
treated urban wastewaters. The observed deterioration is not only due to better monitoring, though. Wastewater discharges are increasing in 
a majority of river basins, namely in the Morava RBD + 7.6%, in the Vltava RBD + 5.7% and in the Oder RBD + 1.7%.The majority of 
substances causing failure to achieve good status in rivers and makes are PBTs. Czechia expects that by 2027 only 38% SWB can reach a 
good chemical status. Overall, the improved monitoring between 2nd and 3rd RBMP have put Czechia in a better position than before to 
identify the root causes for the chemical pollution of its rivers and lakes. This challenge is signficiant.   

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Ground Water 
Bodies   

Trend (% good 
status/potential)  

100%

Main Pressures & Changes & Exemptions  

93,7%

68,9%

2015 2021

Czechia reported a significant numerical improvement of the quantitative status of its groundwater bodies. This seems mainly due to 
improved knowledge, as 21% of GWBs were re-classified from "unknown" status to "good" status. 3.5% of GWBs were re-classified from 
previously poor to good status since the 2nd RBMP. It remains unclear, however, how far these improvements are reliable as 83% of 
assessments are now conducted with medium to low confidence, only. Moreover, Czechia’s approach to classifying ground water bodies still 
fails to consider also the status of surface water bodies which are connected to the ground water bodies, a significant shortcoming and not 
in line with the WFD requirements. Quantitative pressures on groundwater are caused by water abstractions for public water supply, for 
industrial and for agricultural uses. By 2027, CZ expects that 99.4% of GWBs could reach a good quantitative status. At the same time, 
Czechia also reports that 23 GWB (13%) are at risk of failing to achieve good quantitative status by 2027. Measures were mapped to 
prevent or control groundwater abstractions. At the same time, Czechia also plans new reservoirs and water transfers which could increase 
existing quantitative pressures on groundwater. Specific investments are not listed. 

QUANTITATIVE 
STATUS  

50%

0%

100%

50%

CHEMICAL 
STATUS  

26,4%

0%

0%

2015 2021

Czechia is among the EU Member States with the highest portions of groundwater bodies that fail to achieve a good chemical status due to 
diffuse pollution from agriculture. 89 % of GWB are polluted with pesticides, chloridazon desphenyl, nitrate, metazachlor ESA and 
ammonium. Regrettably, non agricultural pollutants show a sustained upward trend in GWB. The main non-agricultural pollutants are 
arsenic, nickel, cadmium, nitrate and aluminium. 43% of groundwater bodies notably fail good chemical status because of the poor surface 
water quality. PFAS are not yet operationally monitored. 156 GWB (90%) are at risk of failing good chemical status by 2027. Measures 
focus on removal of contaminated sites, as well as pesticide pollution from agriculture, and diffuse atmospheric pollution. 

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2. Horizontal aspects 

2.1 Governance 

Czechia  has  a  two-layers  water  governance,  with  authorities  competent  at  the  national  level 
(Ministries of Environment and Agriculture) and 14 regional authorities.  

Transboundary cooperation: Czechia cooperates with neighbouring countries in the Danube RBD in 
hydrological monitoring and data sharing, as well as in coordinated actions towards hydro peaking, 
minimum flows, reservoir management especially under low flow conditions. In 2021 Czechia referred 
Poland  to  the  European  Court  of  Justice  (case  C-121/21)  for  gaps  in  environmental  impact 
assessment  and  authorisation  of  lignite  mining  activities  on  Polish  territory,  as  well  as  relevant 
consultation processes, with potentially significant impacts on groundwater bodies on Czech territory. 

2.2 Characterization of River Basin District 

Czechia participates in three River Basin Districts which are transboundary and which are all covered 
by international agreements: Elbe (shared with AT, DE, PL), Oder (shared with DE and PL) and Danube 
(shared with DE, AT, SK, HU, SR, RO, BG etc). Czechia’s share of these international RBDs respectively 
is  33.7  %  (Elbe),  5.9  %  (Oder)  and  2.7  %  (Danube).  A  permanent  co-operation  body  and  an 
international RBMP are in place for all IRBDs, too (designated as category 1 cooperation). The Czech 
Republic  published  its  draft  RBMPs,  timetable,  and  work  programme  as  well  as  the  overview  of 
significant water management issues for public consultation as requested during six months. 

Table 1. Overview of Czechia‘s River Basin Districts (RBDs) Source: 3rd RBMPs electronic reporting 

RBD 

Name 

Rivers 

Lakes 

Groundwater Bodies 

CZ1000 

Dunaj/Danube 

278 

CZ5000 

Labe/Elbe 

636 

CZ6000 

Odra/Oder 

131 

TOTAL 

1045 

17 

49 

7 

73 

54 

100 

20 

174 

The  Czech  Republic  has  1118  surface  water  bodies  (1045  rivers  and  73  lakes)  as  well  as  174 
groundwater bodies.  

Pressures  &  Impacts:  Czechia’s  knowledge  of pressures  on  surface  water  bodies  has  significantly 
improved since the 2nd RBMPs when pressures on 70% surface water bodies were still unknown.  

As  regards  Surface  Water  Bodies  (river  and  lakes),  Czechia  reports  that  most  significant  are  the 
diffuse pressure from discharges not connected to the sewerage network affecting 74 % of surface 
waterbodies. This is closely followed by diffuse pressures from agriculture affecting 67 % of them, 
and then point pressures from urban wastewater affecting 56 % SWBs. This compares to the 2nd 

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RBMPs  when  70%  SWBs  were  still  reported  to  be  subject  to  unknown  pressures,  a  significant 
improvement of knowledge.  

These improved insights in pressures also allowed Czechia to improve its assessment of impacts. The 
most significant impact on surface water bodies is nutrient pollution affecting 82 % of all SWBs. In 
the  2nd  RBMPs  nutrient  pollution  was  still  being  reported  to  affect  only  41  %  of  SWBs.  Nutrient 
pollution  regularly  stems  from  diffuse  pressures  from  agriculture  (fertilizers)  and  insufficient 
wastewater treatment at industrial sites and in municipalities. Nutrients often cause eutrophication 
of rivers and at times also algal bloom which kills fish due to a lack of oxygen. Czechia’s lakes also 
severely struggle with eutrophication due to the high amount of nutrients (carp farms).  

Czechia’s nutrients concentrations are high across the entire country, with more than 10 mg/l of NO3 
measurements.1 Under pressures from industrialised large-scale agriculture that relies excessively 
on fertilisers, Czechia’s nutrient pollution has increased between 2000 and 2017 from for nitrates/ 
65 to 101 kg N/ha. The latest data suggest that Czechia discharges 179.8 kg N per hectare.2 

For  groundwater  bodies,  diffuse  pressures  from  agriculture  are  now  also  reported  to  affect  the 
highest  percentage  of  groundwater  bodies,  namely  89  %  (3rd  RBMP)  up  from  60  %  GWBs  (2nd 
RBMPs), a pronounced increase. This is followed by point source pressures from contaminated sites 
or abandoned industrial sites and then diffuse pressures from atmospheric deposition. Turning to the 
impacts, the most significant  impact on groundwater bodies is chemical  pollution, affecting 91 % 
GWBs  (3rd  RBMP),  up  from  73  %  GWBs  (2nd  RBMP)  –  again  a  very  pronounced  increase  also  of 
impacts, and aligned with the significant increase of pressures.  

Czechia’s GWBs are regularly polluted with pesticides, chloridazon desphenyl, nitrate, metazachlor 
ESA and ammonium. Nutrient pollution affects also close to 60% GWB. Non-agricultural pollutants 
regrettably  show  a  sustained-upward  trend  in  GWBs  (arsenic,  nickel,  cadmium,  nitrate  and 
aluminium). 

Czech Republic’s utilised agricultural area amounts to 45% of the total land area with major outputs 
of the agricultural industry  including cereals (22.3%), milk (19.7%), and industrial  crops (14.8%).3 
Agricultural landscape is subject to very intense farming practices on particularly large areas with an 
excessive use of nitrogen and phosphate fertilisers.  As a result of erosion wash off, nutrients and 
pesticides from agricultural soil leak into groundwater and surface water bodies.4 Czechia features 
one  of  the  highest  average  size  of  farms  in  the  EU.  There  has  been  a  massive  concentration  of 
holdings with around 75% of farmland being cultivated by large farms. 47% of Czechia’s agricultural 
land is threatened by water erosion, and 49% suffers from high soil compaction due to the large 
proportion of erosion-sensitive crops in crop rotation, large mono-cropped parcels, missing small-
scale landscape variation, and the effects of regulation of water streams. 5  

It is also important to note in this context that more than 70 % of agricultural land in Czechia is 
today  economically  exploited  by  economic  operators  other  than  the  land  owners  (for  historic 
reasons).6 While a farmer who grows crops on his/her own land has inherent incentives to preserve 
the quality of the soil in the long term, thinking often also a generation ahead, a (large) tenant who 

1 Source: JRC, available at 24 (europa.eu).  
2 24 (europa.eu).  
3 Commission Report on the implementation of Directive 91/676/EC on 2016-2019 time period.  
4 See the National Biodiversity Strategy of the Czech Republic 2016–2025 at page 61, prepared under supervision of the 
Ministry of the Environment, page 70, available here. 
5 Czechia’s CAP Strategic Plan available here.  
6 https://mze.gov.cz/public/portal/en/mze/soil/land-ownership-and-land-
prices#:~:text=Rental%20%E2%80%93%20tenure,the%20lowest%20in%20mountainous%20areas. 

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rents  (many  small  land  units)  on  a  short  term  basis  is  tempted  to  maximise  cashflow  only, 
irrespectively  of  long  term  repercussions  for  the  soil  they  rent.  In  a  country  with  such  a  peculiar 
economic situation like Czechia, governmental controls over the sector’s compliance with restrictions 
on  pesticides  and  fertilisers  gain  particular  importance.  Fines  must  be  sufficiently  dissuasive  and 
controls particularly effective.  

It is certainly positive that Czechia’s government strives to increase organic agriculture to reach 21% 
by  2027.  If  achieved,  this  could  be  an  important  step  to  help  reduce  pollution  of  surface  and 
groundwater water bodies alike.  

Wastewater and mine water discharges are also still significant pressures on rivers in Czechia and 
progress to reduce these pressures remains heterogenous. In 2019, a total of 1,522.3 million m³ of 
wastewater and minewater were discharged into surface water bodies, a year-on-year decrease by 
approximately 1.2% according to the Czech government. However, the development of wastewater 
discharges varies according to the RBD. A high increase of wastewater discharges was recorded in 
the Morava RBD (by 7.6%), in the Vltava RBD (by 5.7%) and in the Oder RBD (by 1.7%). Other river 
basin districts to the contrary recorded a decrease in wastewater discharge, the Elbe RBD by 9.4% 
and Ohře RBD by 2.7% (data from 2019).7  

Invasive  alien  species  exert  pressure  on  the  ecological  status  of  surface  water  bodies.  Data  on 
invasive  species  in  Czechia’s  Biodiversity  Strategy  suggest  that  595  alien  animal  species  live  in 
Czechia with 113 of them being considered invasive. Of crayfish considered an invasive species of 
European Union concern, at least three species are procreating in the Czech Republic. These are the 
signal  crayfish  (Pacifastacus  leniusculus),  the  spiny-cheek  crayfish  (Orconectes  limosus  –  high 
fecundity, omnivore, copes with polluted canals), and marbled crayfish (Procambarus fallax – high 
reproductive  potential,  native  to  Northeastern  Mexico,  may  have  significant  impact  on  fish 
populations).  In  particular  the  omnivore  spiny-cheek  crayfish  and  the  signal  crayfish  are  widely 
present in the Czech Republic. The marbled crayfish stayed so far local around Prague and Pardubice, 
but it has a particularly high procreation potential.   

7 REPORT ON WATER MANAGEMENT IN THE CZECH REPUBLIC IN 2019 by the Czech Ministry of Agriculture and the 
Ministry of the Environment , on page 45. 

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Figure 1. Map of invasive cray fish species in the Czech Republic (2023) 

Source: Jiří Picek, Jitka Svobodová and Silvie Semerádová, TGM WRI, p. r. i., May 2023. 

It therefore appears advisable for Czechia to adopt more aggressive measures for containing the 
spreading of invasive crayfish. Such measures can include the release of predator fish that feast on 
invasive  crayfish,  such  as eel,  burbot,  pike perch,  catfish,  chub,  as  well  as  dragonfly  larvae,  which 
successfully destroy juvenile crayfish. Other methods include the sterilization of males or emptying 
fish ponds to allow them to freeze during winters. 8 

Impacts: The most significant impact on surface water bodies is nutrient pollution which affects 82% 
of surface water bodies. This is a notable increase since the 2nd RBMPs where nutrient pollution was 
still reported to affect 41 % SWB. The reason for this increase is not clear from the information in 
the RBMPs.  

8 In this respect see the article here.  

10 

 
 
 
Figure 2. Pressures on Czechia’s surface water bodies (2021) 

Source: WISE electronic reporting 

The most significant impacts on groundwater bodies are chemical pollution which affect 91% GWB 
(2021),  up  from  73  %  GWB  in  the  2nd  RBMP  (2015).    These  GWBs  are  polluted  with  pesticides, 
chloridazon desphenyl, nitrate, metazachlor ESA and ammonium. Nutrient pollution affects close to 
60% GWB. Non-agricultural pollutants showing a sustained-upward trends in GWB are arsenic, nickel, 
cadmium, nitrate and aluminium. 

Figure 3. Pollution of Czechia’s Groundwater Bodies (2021) 

Source: WISE electronic reporting  

Classification: All water bodies have been classified for ecological status or potential but half of the 
river water bodies which are classified in national types do not correspond to any intercalibration9 

9 Intercalibration is essentially about making sure that every EU Member State uses the same yard stick to evaluate the 
status of a surface water body. The intercalibration exercise involves allocating rivers and lakes to commonly agreed 
classes and types so that waterbodies can be compared.  

11 

 
 
 
 
 
types.  Also,  no  type-specific  reference  conditions  have  been  established  for  hydromorphological10 
quality elements of lakes.  

It is worth noting that Czechia has an important cultural heritage in a high number of fishponds that 
can occupy important surfaces (1ha- several hundred ha), some are even in Natura 2000 areas. Main 
fish being farmed is the carp, that supports rather high nutrient conditions. Czechia is aiming to co-
fund the restoration of fishponds that have neglected or flood damaged infrastructure and therefore 
are contributing to increased flood risks. The fish farms, if extensive, can get support for restoration 
if this contributes to reducing flood risks and is complying with the WFD. Historically, Czechia’s high 
number of heavily modified lakes and artificial lakes goes back long ago (14th -20th century) when 
the Czech Republic built a network of ponds and the popular Vltava Cascade with the dams of Kamýk, 
Orlík and Slapy which are now recreational areas with camps, small hotels, restaurants, pubs and 
other  facilities.  There  are  also  approximately  24  000  fishponds  and  water  reservoirs  with  total 
surface area of approximately 52 thousand ha in the Czech Republic where around 20 986 tonnes 
of marketable fish are caught (2019).11 

3. Policy elements contributing to biodiversity and 

climate change adaptation 

3.1 Surface Water: what is their ecological status or potential 

Monitoring 

Czechia’s  knowledge  of  pressures  on  the  ecological  situation  of  surface  water  bodies  has 
considerably  improved  since  the  previous  2nd  RBMP,  when  CZ  still  did  not  know  which  pressures 
affected 70 % of its surface water bodies. This much better insight is due to better monitoring.12 First, 
the  coverage  of  Czechia’s  monitoring  programme  has  increased  since  the  2nd  RBMP.  In  the  3rd 
RBMPs, Czechia’s surveillance monitoring covered 13 % of river water bodies (8 % in the 2nd RBMPs) 
and 48 % of lake water bodies (10 %). For the coverage of operational monitoring, the percentages 
for river and lake water bodies are 96.5 % (95 % in the 2nd RBMPs) and 100 % (78 %), respectively. 
Second, the number of monitored parameters has also increased.  

However, detailed information on these changes has not been provided and it is unclear whether the 
reported increase in monitored parameters concerns both surveillance and operational monitoring. 
There are namely 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.  

Despite the improvements, some significant gaps remain for monitoring quality elements relevant to 
the  ecological  status  of  SWBs.  Czechia  for  instance  does  not monitor biological  quality  elements, 
macrophytes, phytobenthic or benthic invertebrates and fish in lakes, nor their salinity and nitrogen 
conditions.  For  rivers,  the  general  physico-chemical  quality  elements13,  transparency  and  salinity 

10 Hydromorphology considers the physical character and water content of water bodies. Good hydromorphological 
conditions support aquatic ecosystems (i.e. hydromorphological elements such as water flow and substrate provide 
physical habitat for biota such as fish, invertebrates and aquatic macrophytes). 
11 Czechia did not include fishponds in reporting under the RBMP as only 73 lake water bodies were reported 2021 under 
the 3rd RBMP.  
12 Ecological status (or ecological potential for heavily modified surface water bodies) is assessed by monitoring biological 
quality elements with supporting hydromorphological and general physico-chemical quality elements. 
13 Physico-chemical elements include thermal conditions, oxygenation conditions, acidification status and nutrient 
conditions. 

12 

 
 
conditions  are  not  monitored  either.  The  monitoring  of  physico-chemical  elements  would  be 
important as it could allow Czechia to identify also pressures from nutrient pollution.  

Figure  4.  Missing  parameters  for  designating  ecological  status  of  SWB  (without  biological  quality 
elements  (noBQE),  hydromorphological  quality  elements  (noHYMO),  general  physico-chemical  quality 
elements (noPHYSCHEM), or river basin specific pollutants (noRBSP) for classification of ecological status 
/ potential in 3rd RBMP) 

Source: WISE electronic reporting 

Ecological Status 

Czechia  reported  that  changes  between  the  3rd  RBMP  and  2nd  RBMP  make  direct  comparisons 
difficult  due  to  changes  in  the  delineation  of  the  water  bodies,  due  to  stricter  limits  for  physico-
chemical elements (e.g.: nutrients), and due to significant improvements to monitoring (see above).  

Based  on  the  reported  data,  Czechia’s  problems  with  nutrient  pollution  in  rivers  and  lakes  are 
worrying. While previously Czechia reported 18.8 % SWBs in good ecological status (2nd RBMP), this 
has declined to only 5.9 % (3rd RBMPs). The percentage of surface water bodies in moderate, poor, 
and bad status for the current cycle also increased (at the expense of good status) from 70 % in the 
2nd RBMPs to 94.1% in the 3rd RBMPs. Again, this may be due to better insight rather than a genuine 
deterioration over a five years timespan, but the numbers are of concern.  

13 

 
 
Figure 5. Ecological status of SWB in 2nd and 3rd RBMPs 

Source: WISE electronic reporting 

In  particular  Czechia’s  lakes  severely  struggle  with  eutrophication  due  to  the  high  amount  of  
nutrients. Czechia’s nutrients concentrations  are high across the entire country, with more than 10 
mg/l of NO3 measurements.14 Under pressures from industrialised large-scale agriculture that relies 
excessively on fertilisers, Czechia’s nutrient pollution has increased between 2000 and 2017 from 
for  nitrates/  65  to  101  kg  N/ha.  The latest  data  suggest  that  Czechia  discharges  179.8  kg  N  per 
hectare.15 

Figure 6. Trophic Status reported under the Nitrates Directive 

Source: JRC Statistics reported under the Nitrates Directive: trophic status surface water 

14 Source: JRC, available at 24 (europa.eu).  
15 24 (europa.eu).  

14 

 
 
 
 
 
In rivers, potentially also due to eutrophication and/or hydromorphological alterations, the status of 
fish and benthic invertebrates16 is of concern. Both quality elements display a significant percentage 
in poor and even bad status.  

Gap to target 

Czechia’s gap to the 2027 target is profound. Until 2027, the Czech government predicts that the 
ecological status/potential of surface water bodies may improve slightly with only 12.2 % of water 
bodies  achieving  good  or better  ecological  status/potential.  This  implies that  87.8%  SWB  will  fail 
good ecological status by 2027. 

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.  

In the 3rd RBMP, the number of heavily modified river water bodies in Czechia has increased from 
previously  89  (8.5  %)  to  98  (9.4  %).  Often  flood  protection  structures  are  the  cause  for  heavy 
modifications to river water bodies, followed by hydropower. Fisheries and aquaculture, tourism and 
recreation, and urban development each represents 20% of HMWB designations. The main physical 
alterations  related  to  heavily  modified  river  water  bodies  are  channelisation,  straightening,  bed 
stabilisation, and bank reinforcements. For heavily modified lake water bodies, the main alterations 
are weirs/dams/reservoirs. 

Table 2. Heavily Modified & Artificial Water Bodies (CZ, 2021) 

Modifications 

Rivers 
(% of total) 

Lakes 
(% of total) 

HEAVILY MODIFIED   

ARTIFICIAL   

9.4% 

0.5% 

94.5% 

5.5% 

It is striking that 94.5% or river bodies remain natural whereas all lakes are either heavily modified 
or  even  artificial.  .  Czechia  has  a  tradition  of  breeding  carp  in  large  fishponds  which  can  occupy 
important surfaces. Feed-based carp farming can cause eutrophication of a lake’s waters.  

In 2023 it was reported that the Czech Republic is also exploring a possibility of transporting water 
from the Danube in Austria to Czechia for irrigation of farmland in the neighbouring Moravia and 
Lower Austria regions.17 Infrastructure projects of such magnitude could alter the flows of the Danube 

16 Benthic invertebrates are the small animals, such as clams, worms, and crustaceans that live on or in the bottom 
substrate of a water body. These organisms are an important food source for many fish and crustaceans, including many 
recreationally and commercially important species. 
17  
See also at Vyprahlou jižní Moravu může spasit kanál z Dunaje, s nápadem přišlo Rakousko - iDNES.cz. 

15 

 
 
 
 
and  affect  its  ecological  status,  making  an  environmental  impact  assessment  necessary  for 
evaluating the cumulative conditions of Article 4 (7) WFD. This analysis should be conducted as part 
of  an  integrated  river  basin  management  and  be  reflected  in  the  transboundary  River  Basin 
Management Plan for the Danube. The hydrological conditions and the need to guarantee ecological 
flows  of  the  Danube  would  need  future-proofing  in  view  of  climate  change  and  glacier  melting  / 
reduced snowfall. 

3.3 Groundwater bodies - have they sufficient water – quantitative status 

Monitoring 

There  are  1610  monitoring  sites  for  quantitative  monitoring  in  the  3rd  RBMPs.  The  number  has 
increased from 1559 in the 2nd RBMPs. There has been an improvement of knowledge, because no 
groundwater bodies are still assessed in “unknown” quantitative status in the 3rd RBMPs, while 37 
GWB (i.e., 21.3 %) were still assessed as “unknown” in the 2nd RBMPs. In view of these advances, it 
is all the more striking that Czechia’s confidence in the overall quantitative classifications of ground 
water bodies has significantly decreased since the 2nd RBMP. In the 3rd RBMP, most classifications 
are done with “medium” confidence. In the 2nd RBMP, 62.6% GWB were classified with a “high” level 
of confidence, while in the 3rd RBMP merely 16.7% are classified with high confidence.18  Taking these 
numbers  together,  it  seems  that  at  the  2nd  RMP,  Czechia’s  high  confidence  was  probably  due  to 
classifying many GWB as “unknown” while in the 3rd RBMP the “medium” level of confidence is due 
to the fact that now more GWB have been attributed a status albeit for the first time and hence with 
less confidence than before the ”unknown” status.  

Figure 7. Confidence in quantitative status assessment GWB in Czechia  

Source: WISE electronic reporting 

Quantitative Status 

In the 3rd RBMP, 93.7% GWB were in good quantitative status (163 out of 174 GWB). Compared to 
the 2nd cycle, 21% of GWB previously in “unknown” status were re-classified as in “good” status, 
leading to the significant increase from ca. 69% to 93.7% GWB in  good status. At the same time, 

18 The low level of confidence in the assessment of the quantitative status could potentially be due to the fact that 
Groundwater associated aquatic ecosystems  and Groundwater dependant terrestrial ecosystems   are still not considered 
in the assessment of quantitative status of groundwater bodies in all RBDs.  

16 

 
 
 
less GWB were classified in “poor” status, namely only 11 GWB (2021) of previously 17 GWB (2015). 
As  set  out  above,  most  quantitative  status  assessments  were  made  with  lower  confidence  than 
previously.  

There are indeed severe gaps in the assessment methodology and implementation, including lack of 
consideration of GWAAEs, GWDTEs and saline or other intrusions in the assessment of groundwater 
quantitative status in all RBDs. This gap weakens the robustness of Czechia’s assessment. Applying 
a  correct  methodology,  more  ground  water  bodies may  have  to  be  classified  in  poor  quantitative 
status.  

Figure 8. Quantitative Status GWB Czech Republic (2021) 

Source: WISE electronic reporting 

Gap to target 

The Czech Republic expects that by 2027 only one GWB would still fail to reach good quantitative 
status, this would be less than 1%. From Czechia’s programme of measures, it is however not clear 
how the significant improvement from 6.3% to 1% good status will be achieved concretely.   

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

Currently, 21.9% of Czechia’s terrestrial territory is designated as protected areas, slightly below the 
EU value of 26.4%. The EU Biodiversity Strategy has set a target of reaching 30% protected area 
coverage at the EU level by 2030. 

Table 3. Protected areas per type of area and associated water body (CZ, 2021) 

Protected area type 

Number of Water Bodies Associated with protected areas in 

17 

 
 
Rivers 

Lakes 

Groundwater 

26 

32 

34 

165 

125 

Bathing waters 

74 

Drinking water 
protection area 

341 

Other protected habitat 
sites 

683 

Source: WISE electronic reporting 

Monitoring 

Czechia addressed a previous Commission recommendation on covering all relevant protected areas 
and Czechia now reports a large network of protected areas in the 3rd RBMPs. Protected areas have 
been  identified  for  surface  waters  under  the  Bathing  Waters  Directive,  and  for  surface  and 
groundwaters as Drinking Water Protection Zones and Natura 2000 sites which includes the Birds 
and Habitats Directives. 

Gap to Target 

Since the 2nd RBMP, the ecological status of surface water bodies associated with protected areas 
has  deteriorated,  and  consequently  a  number  of  water  bodies  was  re-classified  from  good  to 
moderate status. The chemical status has followed a similar downward trend. Now less than 40% of 
water bodies associated with protected areas remain in good chemical status, compared to 75% in 
the 2nd RBMPs. Again, due to better monitoring, a more realistic picture of reality has emerged since 
the 2nd RBMP, visualised in the below chart.  

Figure 9. The status of water bodies associated with protected areas in 2022 

0%

2022

20%

40%

60%

80%

100%

Ecological status/potential SWB

e
p
y
T
s
u
t
a
t
S

Chemical status SWB

Chemical status GWB

Quantitative status GWB

% of water bodies associated with PAs

High

Good

Moderate

Poor

Bad

Unknown

18 

 
 
 
 
Source: Member State WISE electronic reporting 

Measures 

Member  States  are  required  to  set  additional  environmental  objectives  and  standards  for  water 
bodies  linked  to  protected  areas  where these  are  needed  to  ensure that the requirements  of the 
Directives applicable to those protected areas are met. However, no information was found within 
Czechia’s  3rd  RBMPs  related  to  such  additional  objectives  for  protected  areas.  To  the  contrary, 
additional measures have been planned in the 3rd RBMPs relating to Birds and Habitats Directives for 
surface and ground waters. 

3.5 What is being done to prevent/reduce hydromorphological pressures 

Monitoring 

Czechia  deserves  credit  for  comprehensively  mapping  morphological  alterations  to  surface  water 
bodies since the 2nd RBMP. A new and improved method has been developed taking account of CIS 
Guidance  No.  4  and  Commission  recommendations  on  the  designation  of  heavily  modified  water 
bodies in the 2nd RBMPs. 

Measures  

The 3rd RBMP is less convincing when it comes to mitigation measures. The Plan contains only some 
limited  information  on  restoration  and  mitigation  measures  which  are  only  briefly  described  in  a 
qualitative  way.  Background  documents  mention  that  mitigating  hydropeaking  and  ensuring 
minimum flows in the reservoirs are in place as they were required by legislation at the time when 
the dams were built (1960s  – 1980s). Programmes to support the revitalisation of watercourses, 
water retention in the landscape and the recovery of landscape structures are referred to in Czechia’s 
Report on Biodiversity where however it is also noted that the measures are often not sufficiently 
implemented. 19   

It is unclear whether Czechia’s legislation foresees the periodic review of water permits including 
permits for irrigation. There is no explicit link in the 3rd RBMPs between the implementation of e-
flows and the authorisation process and / or review of permits to control water abstractions. At the 
time of the 3rd RBMP, a new methodology  for e-flows was still awaiting approval. The 3rd RBMP 
foresees a number of measures to tackle ecological pressures. They KTM5 – Improving longitudinal 
connectivity,  KTM6  –  Improving  hydromorphological  conditions  of  water  bodies  other  than 
longitudinal continuity and KTM7 – Improvements in flow regime and / or establishment of ecological 
flows. Assessment and tackling of these pressures have been improved compared to the previous 
cycle thanks to a new comprehensive database of hydromorphological mapping.  

It  is  very  positive  that  Czechia  cooperates  with  neighbouring  Austria  to  re-naturalise  –  with  EU 
financial support - transboundary rivers like Thaya in order to restore spawning grounds for local fish 
populations. 20 

19 See the National Biodiversity Strategy of the Czech Republic 2016–2025 at page 50, prepared under supervision of the 
Ministry of the Environment, page 70, available here.  
20 https://2014-2020.at-cz.eu/at/ibox/pa-2-umwelt-und-ressourcen/atcz7_dyje-2020-thaya-2020. 

19 

 
 
3.6 What Czechia is doing for abstractions and water scarcity 

As in the previous 2nd cycle, Czechia has not identified water abstraction as a significant pressure at 
the RBD level or in significant portions of any RBD. However, according to the EEA’s Water Exploitation 
Index21, 19.5% of all freshwater in Czechia is consumed in some form. This is just underneath the 
20% threshold above which a country usually experiences water scarcity.22 It must be  noted that 
groundwater  abstractions  have  been  declining  between  1989  and  2006,  and  stayed  stable  since 
then. However, according to an analysis by the Czech Ministry of Agriculture in 2019, groundwater 
abstractions have been increasing in the Oder RBD by 1.7%. 23 

Regarding basic measures to control abstraction from surface and groundwater (referred in Article 
11(3)(e) WFD), in Czechia there is a concession, authorisation, and / or permitting regime to control 
surface and groundwater abstractions and impoundments. Furthermore, there is an updated register 
of abstractions from surface water and groundwater and a register of impoundments. For smaller 
abstractions no registration and reporting are required; these are abstractions below 100 m3/month 
or 1000 m3/year, and where the volume of water raised or stored by a water body does not exceed 
1 000 000 m3.24  Permits  are  generally  issued  for  a  fixed  limited period,  which may  be  longer  for 
hydropower projects (>30 years) and impoundment/accumulation water works (valid for the duration 
of the use of the structure).  

Regrettably, the Czech Republic has not yet defined a methodology for ecological flows. Ecological 
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 must be granted knowing the minimum flows of 
surface water bodies that connect with ground water bodies.25 

3.7 Adaptation to climate change 

As regards flood risks, the Floods Directive requires Member States to consider the impact of climate 
change on the occurrence of floods, and therefore in the preparation of Flood Hazard and Risk Maps 
(FHRMs) and Flood Risk Management Plans (FRMPs). More information on these Maps and Plans can 
be  found  in  Section  B.  However,  considering  the  close  relationship  between  overall  water 
management and floods management and the importance of climate change on both, theytheythey 
are jointly addressed in this section.  

21 The WEI+ provides a measure of total water consumption as a percentage of the renewable freshwater resources 
available for a given territory and period. The WEI+ is an advanced geo-referenced version of the WEI. It quantifies how 
much water is abstracted monthly or seasonally and how much water is returned before or after use to the environment 
via river basins (e.g. leakages, discharges by economic sectors). The difference between water abstractions and water 
returns is regarded as ‘water consumption’. 
22 It is noted that the raw data underlying the calculation of WEI+ have some shortcomings. 
23 REPORT ON WATER MANAGEMENT IN THE CZECH REPUBLIC IN 2019, Ministry of Agriculture of the Czech Republic and 
Ministry of the Environment of the Czech Republic, on page 47.  
24 Water Act – Section 8 and 10, Decree No 431/2001 Coll. and Methodology for the assessment of significant pressures 
stipulate that authorised people holding a water management permit are obliged to measure the quantity and quality of 
the abstracted water, the volume of water raised and the volume of water stored, and submit the results to RBD authorities 
by reporting annual data to the Records of abstractions, discharges and impoundments/accumulations of water for water 
balance. No registration and reporting are required, if water abstraction exceeds 100 m3/month or 1000 m3/year, and 
where the volume of water raised or stored by a water body exceeds 1 000 000 m3. 
25 See Annex II, section 2.1.2 definition of quantitative status  

20 

 
 
A national research project and studies on impact of climate changes (dated 2015 and updated in 
2019) on maximum discharges indicate no significant and robust trend that would point to changes 
in flood events in the next few decades. Therefore, the impact of climate change was not considered 
in flood scenario preparations. Czechia’s second FRMPs state that the outputs of climate models are 
very  uncertain  and  vary  between  scenarios  and  models.  The  FRMPs  note  that,  while  total  annual 
precipitation is expected to increase in northern Europe and decrease in southern Europe, Czechia lies 
in between. The plans then go on to state that deciding on possible adaptation measures for flood 
risks in the country faces large uncertainties. The sources for this analysis are not identified, however. 
The second FRMPs moreover do not refer to specific climate change scenarios or to quantitative or 
qualitative analyses of the potential impacts of climate change on floods. Overall, the assessment of 
potential  climate  impacts  on  flooding  in  Czechia  has  not  changed  compared  to  the  first  FRMPs. 
Perhaps as a consequence, the FRMPs do not identify measures specifically to address the expected 
effects of climate change on flooding; the plans do, however, state that technical solutions should 
give  preference  to  structures  enabling,  in  the  event  of  a  change  in  conditions  in  the  future, 
adaptability to allow an additional increase in their protection at an acceptable cost.  

As  regards  drought  risks  and  water  scarcity,  like  many  other  EU  Member  States,  also  the  Czech 
Republic  suffers  from  droughts.  The  severe  drought  of  2020,  for  instance,  exposed  every  5th 
municipality in Czechia to water scarcity, particularly in the regions of Southern Moravia and in the 
Northwest.26 It is therefore welcome that Czechia’s 3rd RBMP considers the national climate change 
adaptation  strategy  for  designing  the  3rd  RBMPs  programme  of  measures.  Czechia’s  National 
Adaptation Strategy is referred to in the 3rd RBMPs as guidance for measures27, and Czechia also 
drew  up  a  "Concept  for  protection  against  the  effects  of  drought  for  the  territory  of  the  Czech 
Republic” which recommends the creation of a proper drought risk management plan.  

Moreover,  in  preparation  for  the  3rd  RBMP  cycle,  a  baseline  scenario  for  climate  induced  water 
impacts until 2045 was prepared. This baseline scenario until 2045 was then used to model various 
scenarios  on  potential  impacts  of  climate  change  on  water  management  in  Czechia.  This  in  turn 
served then as a basis for developing programs of measure.28 Finally, in the IRBMPs, specific chapters 
are also present which analyse the effect of climate change on significant pressures and water status, 
whilst also establishing transregional objectives for climate change adaptation.  

It is also positive that Czechia in 2020 amended its Water Act to set up an operational governance 
for manging  water  scarcity.  Regional  commissions  can  now  declare  a  state  of  water  scarcity  and 
impose restrictions on the use of water in the event of droughts. The amended Water Act introduced 
a requirement to develop plans for water scarcity and droughts at the regional and at the national 
level.  

Eventually, successful climate mitigation and adaptation for water management will also necessitate 
measures  beyond  those  referred  to  in  the  3rd  RBMP  Programme  of  Measures,  or  in  the  FRMPs, 
because the water cycle is significantly affected by sectoral policies outside the scope of the WFD. To 
prevent that ground water is being depleted for irrigation in agriculture (for instance in the Morava 
region), resilience should be improved through nature-based solutions that improve water retention 
in the landscape, by promoting less water-intensive crops and through water reuse. This all would 
help Czechia secure the long-term resilience of its agricultural sector to climate change.29 Moreover, 
there  seems  to  be  scope  for  improvements  to  Czechia’s  forestation  policies.  Monocultures  of 

26 https://www.osw.waw.pl/sites/default/files/OSW-Report_Drought-in-the-Czech-Republic_net.pdf 
27 "Measures to prevent and mitigate the effects of drought and water scarcity", which are based on the document 
"Concept for protection against the effects of drought for the territory of the Czech Republic" Mezirezortní komise VODA-
SUCHO (2023) Koncepce ochrany před následky sucha pro území České republiky na období 2023–2027. 
28 https://eagri.cz/public/web/file/694664/LABE_II_VLIVY_A_DOPADY.pdf  
29 See the Report from the Commission to the European Parliament and Council ”Summary of CAP Strategic Plans for 
2023-2027: joint effort and collective ambition”, page 7 of 23.11.2023, COM(2023) 707 final. 

21 

 
 
coniferous trees account for around 70% of the country’s forests. They are particularly vulnerable to 
high temperature and temperature fluctuations. This  has exposed Czechia’s forests to bark beetle 
invasions. In recent years, the necessary logging covering vast stretches of forest has significantly 
aggravated soil erosion.30 In addition, Czechia’s State of the Environment report mentions that the 
increasing extent of land sealed by constructions disrupts the ability of the landscape to retain water 
and protect against floods.31  

4. Policy elements contributing to zero pollution 

4.1 Surface Water: what is their chemical status 

Monitoring 

According to the electronic data reported by Czechia under the 3rd RBMPs, for 84% of rivers are now 
subject to operational monitoring, but the monitoring of lakes covers 47 % only, down from 58% in 
the 2nd RBMP, a significant decline. Surveillance monitoring covers 13.2% and 19.6% of rivers and 
lakes respectively. As monitoring of lakes declined, knowledge about their chemical status declined, 
too. The chemical status is now, regrettably, unknown for as much as 44% of all lakes.  

Table 4. Percentage of surface water body (length / area) included in monitoring  

Chemical status monitoring 

3rd RBMPs 

River length % 

Surveillance monitoring 

River length % 

Operational monitoring 

Lake area % 

Surveillance monitoring 

Lake area % 

Operational monitoring 

Source: WISE electronic reporting 

Gap to Target 

13.2% 

84.0% 

19.6% 

47.0% 

According to electronic reporting, in 2021 only 38.6% SWB are in good status, which means that 
Czechia still has a gap of 62% SWB not in good status, of which 18.4% are in unknown status. 42.9% 
of  surface  water  bodies  are  in  poor  chemical  status,  up  from  30%  in  the  1st  and  2nd  RBMPs. 
According to the Czech government this increase in “poor” status reflects a stricter methodological 
approach  based  on  the  precautionary  principle  rather  than  a  substantial  deterioration.  Looking 
forward to 2027, data received through WISE reporting suggest that the Czech Republic expects to 
achieve  good  chemical  status  for  another  6  SWB  by  this  date.  This  also  means  that  only  limited 
progress is expected from the measures now planned in the 3rd RBMPs.  

30 https://www.osw.waw.pl/sites/default/files/OSW-Report_Drought-in-the-Czech-Republic_net.pdf.  
31 The State of the Environment Report (SoER) of the Czech Republic is a basic reporting document of the Czech Republic. 
The SoER is published annually on the basis of Act No. 123/1998 Coll (as per EEA, 2015). 

22 

 
 
Figure 10. Chemical Status SWB in 1st, 2nd, 3rd RBMP  

Source: WISE electronic reporting 

Compared to the 2nd RBMP, the number of water bodies in unknown status has increased. The Czech 
government  clarified  that  this  is  due  to  several  reasons,  the  main  reason  being  that  gaps  in  the 
monitoring  of  surface  water  bodies  (SWBs)  were  no  longer  closed  using  expert  judgment.  The 
confidence in the classification of 3rd RBMP stayed largely the same as in the 2nd RBMP, the majority 
of water bodies being classified with a medium level of confidence. 

The primary substances that cause failure to achieve good chemical status  of rivers and lakes in 
Czechia are PAHs32, mercury, PBDEs, heptachlor and heptachlor epoxide. Excluding these Persistent, 
Bioaccumulative and Toxic substances (PBT) which have high resistance to degradation, there are 
also  a  number  of  non-PBT  substances  which  cause  failure  to  achieve  good  chemical  status.  In 
particular,  this  includes  fluoranthene  and  two  pesticidal  /  biocidal  substances,  cybutryne  and 
dichlorvos. Cybutryne was used as a biocide, particularly in shipping for treatment of hulls which was 
legal to use in the European Union until 201633. Dichlorvos is an organophosphate insecticide which 
was no longer used in the European Union after 2006.34. In other words, several substances which 
keep polluting Czechia’s surface and groundwaters date back to times when these substances were 
not yet prohibited, they are persistent.  

32 Listed in Figure 4.4 individually as Benzo(a)pyrene, Benzo(g,h,i)perylene, Benzo(b)fluoranthene, and 
Benzo(k)fluoranthene. 
33 COMMISSION IMPLEMENTING DECISION (EU) 2016/ 107 - of 27 January 2016 - not approving cybutryne as an existing 
active substance for use in biocidal products for product-type 21 (europa.eu) 
34 EUR-Lex - 32007D0387 - EN - EUR-Lex (europa.eu) 

23 

 
 
 
Figure 11. Priority substances causing failure of chemical status in SWB (2021) 

One cause for diffuse pollution of surface water bodies is also air pollution coming from combustion 
processes.  Air  pollution  still  remains  a  serious  environmental  and  health  problem  of  the  Czech 
Republic.35 If Czechia tackled air pollution more decisively, it could also reduce pollution of its surface 
water bodies, for instance of mercury. 

4.2 Groundwater Bodies: what is their chemical status 

Monitoring  

The  confidence  in  the  assessment  of  the  chemical  status  of  groundwater  bodies  has  decreased 
(Figure 6-4). Classification chemical status of groundwater bodies with high confidence decreased 
from  87.9  %  in  the  2nd  RBMPs  to  82.8  %  in  the  3rd  RBMPs.  The  rest  of  the  classifications  are 
conducted with medium (8%), low (8 %) or unknown (1.1 %) confidence. The RBMPs do not explain 
this change. 

Chemical Status 

In the 3rd RBMP, only 26.4% (46 out of 174) groundwater bodies remain in good chemical status, 
while the vast majority (126 GWB = 72.4%) are being classified in poor chemical status and 2 GWB 
(1.1 %) unknown status. Since the 2nd RBMPs, 17 GWB have turned from good to poor chemical 
status.  The Czech Republic still fails to consider the status in of GWAAEs and GWDTEs in assessing 

35 HomePage - Ministerstvo životního prostředí (mzp.cz).  

24 

 
 
 
the status of ground water bodies. The number of GWBs in poor chemical status may therefore be 
higher than reported.  

Figure 12. Chemical Status of GWB in the Czech Republic (2021) 

Source: WISE electronic reporting 

Gap analysis 

A key reason why the Czech Republic is failing to achieve good status for so many ground water 
bodies is the chemical contamination of industrial sites. The gap analysis in the 3rd RBMP suggests 
that  137  GWBs  miss  good  status  due  to  “contaminated  sites  or  abandoned  industrial  sites”.  The 
number of priority substances that contaminate Czechia’s groundwater is long. Czechia also has high 
portions  of  groundwater  bodies  that  do  not  have  a  good  chemical  status  due  to  nitrates  and 
pesticides. While nitrate pollution caused 45 GWB to fail good status in 2021, the gap analysis in the 
3rd  RBMP  suggests  that  already  111  GWB  fail  good  status  due  to  pesticides  pollution.  Diffuse 
atmospheric pollution fails 35 GWB from reaching good status. 

4.3 What Czechia is doing to combat pollution from agriculture 

The  most  significant  impact  on  the  ecological  status  of  surface  water  bodies  in  Czechia  remains 
nutrient pollution which affects 82 % of surface water bodies. This is twice as much nutrient pollution 
as in the 2nd RBMPs, where nutrient pollution was reported to affect 41 % of surface water bodies. 
Emissions for N are (also) caused by fossil fuel energy production at household level and by energy 
plants, industry, traffic and agriculture. Czechia has the second highest share (50%) of coal in its total 
domestic  energy  production,  despite  a  36%  decrease  since  200936,  which  contributes  for  an 
important part to the N-pollution.  

36 Czech Republic 2021 – Analysis - IEA 

25 

 
 
 
Generally  speaking,  Czechia’s  Programme  of  Measures  under  the  3rd  RBMP  has  been  further 
developed  compared  to  the  2rd  RBMP  and  more  information  has  become  available  on  the  links 
between measures and pressures. Information is now also presented on the use of cost effectiveness, 
though  this is  still largely focused  on basic  measures,  with  a  bias towards measures  compulsory 
under the Urban Waste Water Treatment Directive, i.e.: measures concerning urban waste waters, not 
pollution from agriculture.  

Czechia’s  Strategic  Plan  for  the  Common  Agricultural  Policy  (“CAP”)37  pays  some  attention  to 
improving water quality. For instance, farmers are incentivised not to apply pesticides in 12-metre 
buffer strips around water courses, which is substantially larger and more effective than the 3-metre 
minimum mandatory under the CAP. In addition, financial support is offered for measures protecting 
the vicinity of four large drinking water reservoirs, covering an area of 25 000 hectares, where only 
limited use of pesticides is allowed. That said, these measures under the CAP remain voluntary, i.e.: 
they do not oblige farmers to actually avoid pesticides and fertilisers.  

Czechia’s CAP Strategic Plan 2023-27 aims amongst others. at redistributing EU financial support to 
small-  and medium-sized  farms,  strengthening  also the  position  of  organic  farming  aiming  for  a 
growth from 16% to 21.3% of the agricultural land in 203038, and improving the vitality and quality 
of life in rural areas through investments. In Czechia about 16% of the total utilised agricultural area 
is already organic farming, which is above EU average in 2021 (ca. 10%)39 but far below the Green 
Deal target for 2030 (25%).  

The  Czech  CAP  Strategic  Plan  in  2022  is  focussing  on  biodiversity  measures,  but  part  of  those 
measures is beneficial for water objectives too, like arable land being dedicated to non-productive 
areas and the sustainable meadow management including sustainable animal grazing. The shift to a 
more sustainable meadow management is expected on more than 25% of the agricultural land. This 
is  reducing  diffuse  pollution  of  nutrients  for  the  water.  The  aim  to  deploy  integrated  production 
methods (limiting pesticides and replacing them with biological preparations) on more than 40.000 
hectares is an important step to further reduce the pesticides pollution. According to Czechia’s CAP 
Strategic Plan, the share of utilised agricultural area (UAA) under supported commitments related to 
improved nutrient management is currently 14.19%; and related to a sustainable use of pesticides 
it is 23.09%.40  

To close the gap, Czechia would need to reduce nutrient loads on 28.365 km2 of agricultural land 
and pesticide pollution on 10.575 km2 of agricultural land.41 However, looking forward to 2027, the 
3rd RBMPs does not offer specific data for how to achieve good status by 2027 for nutrient loads 
from  agriculture  in  specific  water  bodies.  There  is  a  reference  to  the  assessments  done  in  the 
international RBDs, but no data are presented in the RBMPs themselves.  

Similarly, there is no detailed assessment of how the measures from the 2nd RBMP planning cycle 
have been implemented and their efficiency. The more detailed fact sheet on each measure includes 
a description of what the measure might entail, but there are no details of its implementation nor its 
impact. There is only limited reference made to implementation of the Nitrates Directive in the RBMPs.  

37  More  information  about  relevant  measures  can  be  found  in  “Mapping  and  analysis  of  CAP  strategic  plans”  (2023-
2027)  the link Mapping and Analysis of CAP Strategic Plans - European Commission (europa.eu) 

38 At a glance: Czechia's CAP Strategic Plan (europa.eu) 
39 Developments in organic farming - Statistics Explained (europa.eu).  
40Czechia’s Cap Strategic Plan 2021 report, 2023CZ06AFSP001, page 101.  
41 See table A.4 Country report CZ Republic  (” Table A.4 Key Types of Measure planned to achieve objectives in surface 
water bodies by 2021 in the Czech Republic“) 

26 

 
 
The key measures planned in the 3rd RBMP PoM to close the gaps show the magnitude of the issues 
Czechia is facing: KTM2 to reduce nutrient pollution from agriculture for 6030 km2; KTM3 to reduce 
pesticides pollution from agriculture for 14.762 km2.  

Regrettably, Czechia’s Programme of Measures does not foresee measures for the recovery of cost 
of water services in agriculture” nor “advisory services for agriculture” which could be important to 
help farmers to better manage manure.  

Overall, while some progress is being made, that progress is by far too slow for Czechia to reduce 
pollution from agriculture significantly and eventually meet WFD objectives.  

4.4 What Czechia is doing to combat pollution from other sectors 

Nitrate pollution not only emerges in the agricultural sector, but also results from burning fossil fuels. 
Lignite still accounts for almost half of Czechia electricity generation and a quarter of its residential 
heating demand. The burning of lignite causes aerial and surface water pollution. Geographically, the 
most  affected  regions  where  air  quality  standards  are  repeatedly  exceeded  are  in  particular  the 
agglomeration  Ostrava/  Karviná/  Frýdek-Místek,  as  well  as  the  Prague  agglomeration,  Brno 
agglomeration, the Northwest zone (Ústí nad Labem Region), the Central Bohemia zone (Kladno area) 
and the Central  Moravia zone.42 All this aerial pollution exerts pressures on the quality of surface 
water bodies. Czechia has adopted programs for Air Quality Improvement as defined by the Ambient 
Air Quality Directive 2008/50/EC. However, in practice these programs seemingly fall short of what 
is needed to comply with the Directive’s requirements as several infringement cases suggest.   

Beyond nitrate pollution, Czechia identified in total 55 prohibited substances in the Danube RBD, 56 
in the Elbe RBD and 55 in the Oder RBD which include 45 priority substances. To achieve good status 
in surface water bodies in 2021, the Czech Republic would have had to close a very significant gap 
for a large number of prohibited and non-prohibited substances.43 Amongst the polluting substances 
are also highly toxic substances like DDT, lead, arsenic, and uranium. The gap is more significant for 
some substances than for others. As an example, the gaps for DDT (2 SWB), lead (4 SWB), arsenic 
(13 SWB) and uranium (1 SWB) in rivers and lakes is smaller than the gap for Bisphenol A (78 SWB), 
EDTA (93 SWB) and Mercury (95 SWB). 

The key measures planned in the 3rd RBMP PoM to close the gaps show the magnitude of the issues 
Czechia is facing: The 3rd RBMP PoM maps KTM 4 remediation of contaminated sites for 15.772 
km2. There are also 7.167 km2 affected by unknown anthropogenic pressures, addressed with KTM 
14 (research). 

Czechia’s programme of measures prioritises measures that have traditionally been regulated and 
are subject to improvement measures, in particular the Urban Waste Water Treatment Directive. Type 
A measures (that is measures specific to a water body), relate to wastewater plants and sewage 
systems and are prioritised due to their significant impact to address point source discharges (1221 
measures) and diffuse pollution (420 measures). Moreover, 102 measures are planned to phase out 
emissions of priority hazardous substances.  

42 HomePage - Ministerstvo životního prostředí (mzp.cz).  
43 Table A.3 of Czech Country Report.  

27 

 
 
A critical factor for the success of implementing these and other measures will be the availability of 
funding to support investments required. The cost of the measures in the Czech Republic has been 
mapped out, but importantly, the source of funds remains only estimated. For example, the cost of 
measures for CZ1000, CZ5000 and CZ6000 amounts to 68 126 million CZK. The estimated funding 
for these measures comes from EU funds (15 834 million CZK) and the national budget (52 292 
million CZK).44 However, funding cannot be considered ‘secured’ if there are only estimates on funding 
needs  and  indications  about  potential  funding  sources.  Czechia  should  spend  all  programmed 
amounts for sustainable water management under cohesion and regional funds.  

Regrettably, Czechia also does not foresee measures to use water pricing policy for recovering cost 
of water services from industry, while Czechia qualifies the remediation of contaminated sites as 
“disproportionately  expensive”  when  invoking  exemptions  to  justify  non-compliance  with  “good 
status” requirements under Article 4 WFD. 

4.5 What Czechia is doing to combat significant pressures – overall 

assessment of the Programmes of Measures 

Gap assessment  

The Programme of Measures has been further developed in the 3rd RBMP and more information has 
become available on the use of key measures and links between these measures and pressures.  The 
RBMP also includes a gap assessment.  All pressures are associated with KTMs with either basic or 
supplementary measures assigned to them. However, there is limited information on the gap to target 
in 2021 (no information is presented for 2027) and the assignment of indicators to KTMs. The main 
barrier  to  the  effectiveness  of  the  2nd  RBMP  PoMs  has  been  reported  as  a  lack  of  appropriate 
measures. 

Cost-effectiveness  

The RBMP includes information on the cost effectiveness of measures, although this is largely focused 
on  the  basic  measures,  with  a  bias  towards  those  associated  with  the  UWWTD.    Information  is 
presented  on  the  co-ordination  of  the  PoMs  with  other  Directives  and  within  transboundary 
catchments. 

5. Exemptions and economics 

5.1 To what extent are exemptions applied in Czechia 

Since the 2nd RBMP Czechia has improved the use of exemptions at a conceptual level by applying 
exemptions at the level of water bodies. Czechia invokes the exemption of Article 4(4) WFD for the 
chemical pollution of 480 SWB, that is 42.9% of all SWB. Czechia more specifically invoked “technical 
infeasibility” for most of them and for 19 SWBs, that is 1.7 %, “disproportionate cost”. Regrettably, 
the 3rd RBMP does not include any explanation on the reasons to invoke the technical infeasibility or 
disproportionate  cost  at  the  surface  water  body  level,  i.e.  of  the  actual  reasons  justifying  the 
exemption for each water body based on a technical and/or economic analysis. 

44 As of December the 8th 2023 1 CZK = 0.041 Euros. Therefore 68 126 million CZK= 2 796 572 EUR. 

28 

 
 
Table 5. WFD Exemptions used by Czech Republic (3rd RBMP) 

Number of exemptions 

Significant pressure on surface water 

Article4(4) - 
Disproportionate 
cost 

Article 4(4) - Technical  
feasibility 

P1-1 - Point - Urban waste water 

P1-3 - Point - IED plants 

P1-4 - Point - Non IED plants 

P1-5 - Point -Contaminated sites or 
abandoned industrial sites 

39 

P2-10 - Diffuse – Other 

P2-2 - Diffuse - Agricultural 

P2-4 - Diffuse - Transport 

P2-6 - Diffuse - Discharges not connected to 
sewerage network 

14 

9 

13 

39 

1 

15 

60 

13 

P2-7 - Diffuse - Atmospheric deposition 

1052 

P4-2-9 - Dams, barriers and locks - Unknown 
or obsolete 

P7 - Anthropogenic pressure – Other 

P8 - Anthropogenic pressure – Unknown 

1 

38 

74 

As can be seen from the above, Article 4(4) exemptions have been widely applied to water bodies, as 
was  the  case  in  previous  RBMP  cycles.  In  the  3rd  RBMPs,  exemptions  according  to  Article  4(4)  in 
surface waters are applied to 1050 SWBs (93.9 %) for ecological status / potential and to 480 SWBs 
(42.9 %) for chemical status. Exemptions according to Article 4(4) for groundwater are applied to 10 
SWBs (5.7 %) for quantitative status and to 126 SWBs (72.4 %) for chemical status. All Article 4(4) 
exemptions have been justified on the grounds of lacking technical feasibility, disproportionate costs 

29 

 
 
 
 
 
 
 
 
 
 
 
 
 
  
and  /  or  natural  conditions  (the  latter  for  groundwater  bodies  only)  with  type  of  exemption  and 
rationale  indicated  for  each  individual  water  body,  but  without  detailed  justifications  (reported  or 
referred to).  

Regrettably, the 3rd RBMP does not appear to conduct an in-depth economic cost-benefit analysis per 
water body to justify exemptions on grounds of “disproportionate costs” (see economic section at the 
end). Moreover, the possibility to invoke the exemption of Article 4 (4) WFD also expires in 2027.  

According to the 3rd RBMP, no exemptions according to Article 4(6), Article 4(7) and 6(3) have been 
applied in this cycle. Article 4(5) has been applied to 1 groundwater body (0.6 %) for chemical and 
quantitative status on the grounds of disproportionate costs with information provided at the water 
body level, but without detailed justification. 

5.2 Use of economic analysis and water pricing – cost recovery 

In the 2nd RBMP, the Commission recommended to Czechia to apply more rigorously WFD article 9’s 
cost recovery principle unless exemptions according to Article 9(4) WFD apply, and to make it more 
transparent how different water users contribute.  

In the 3rd RBMP, the Czech Republic  

defines water services as “all activities that provide for the abstraction, impoundment, treatment and 
distribution of surface water and groundwater for households, public institutions or any economic 
activity, or for the discharge and treatment of wastewater with subsequent discharge into surface 
waters”. The report disaggregates data for these services as requested by Art 9 (1) WFD according 
to the broad water use sectors households, industry, energy, manufacturing/industry and agriculture..  

Confusingly, the 3rd RBMPs also refers occasionally to “watercourse and river basin management” as 
a distinct water service, while the Czech authorities actually treat it as an “other water use” since it 
does not undergo its own cost-recovery analysis. Instead, the RBMPs indicate that the charges for 
watercourses and river basin management help to cover the expenses associated with the treatment 
of surface water abstracted to source public water supply. 

The 3rd RBMP does not report specific progress on the economic methodology since the 2nd RBMP. 
Following a national methodology, the analysis has been carried out at the national level without a 
differentiation  between  RBDs,  based  on  2018  data.  Most  of  the  assessment  items  listed  in  WFD 
Annex III are reported. There are long-term forecasts of water supply, with breakdown over source 
types,  and  of  water  demand,  categorised  by  water  user  types  and  sectors.  Presumably,  these 
forecasts draw on the ‘baseline scenario for water management, water use and water impact’ up to 
the year 2045, coming from the National Climate Adaptation Strategy. In addition, there are volume, 
cost  and  price  estimates  for  the  broad  water  services  water  supply  and  sanitation  services, 
differentiated by user types / sectors. 

Remarkably, there appear to be no estimates and forecasts for the investments in water supply and 
wastewater collection and treatment facilities, apart from those on the investment measures in the 
Programme of Measures. 

For  the  2021  reporting,  the  quantitative  cost-effectiveness  analysis  (CEA)  has  only  informed  the 
selection  of  the  so-called  “Type A”  measures  related  to  specific  wastewater  plants  and  specific 
sewage systems. The RBMPs say that because of a lack of data, CEA has not been used for other 
type A measures (i.e. other measures targeting specific waterbodies and neither for type B and type 
C measures (respectively a general course of action targeting a significant pressure or with a national 

30 

 
scope).  The  RBMPs  consequently  do  not  compare  the  cost  effectiveness  of  different  types  of 
measures, for example measures addressing nutrient point sources vs those tackling nutrient diffuse 
sources aiming at reducing nutrient input. Cost-Effective  analysis was carried out  only  for certain 
measures related to wastewater plants and sewage systems. 

The RBMPs do not offer a concrete conclusion as to whether the pricing policy provides adequate 
incentives to use water efficiently. However, the RBMPs’ comprehensive outline of the pricing structure 
suggest some incentives with a potential for improvement, as illustrated below. 

The regulatory procedures to set tariffs for collective water supply and sanitation are laid down in 
national legislation. This price regulation is explicitly geared to cover the costs of providing the water 
services: the water companies need to follow binding rules for their cost accounting, the calculation 
of the water service costs and how to set on that basis the tariffs. The tariffs can take two forms: 
either ‘fully volumetric,’ i.e. through a defined unit rate, or ‘mixed,’ i.e. a volumetric and fixed part, the 
latter  depending  on  a  set  of  consumer  profile  parameters.  The  latter  allows  social  tariffs 
arrangements.  

The law also defines the charges to be levied on surface water abstraction above a threshold volume 
and  arranges  that  the proceeds  are  used to  fund  water  management  services.  This  arrangement 
implies that irrigation is priced when sourced from surface water (rather than from groundwater). 
The RBMPs do not report on the pricing of other individual water services. 

The  RBMPs  report  cost  recovery  rates  for  the  collective  water  services,  combined  and  separately.  
These rates are calculated at RBD level on the basis of a national methodology. Next to the financial 
cost  recovery  rate,  they  also  present  so-called  “broader”  cost  recovery  rate  which  include 
environmental costs.  

The financial cost recovery rate calculations have informed the decision to only recover a part of the 
depreciation costs through the water tariffs, as a full recovery would bring the prices up beyond what 
is deemed socially acceptable, thus calling on the socio-economic mitigation factors listed in article 
9 of the WFD. It is not clear whether the non-recovered costs correspond with the amount of financial 
support  from  the  EU  Funds,  and  whether  a  part  of  these  costs  are  perhaps  set  aside  for  future 
recovery (non-linear depreciation). 

There is no clear account in any RBMP on whether the various water uses and user sectors provide 
an  adequate  contribution  to  the  water  services’  cost  recovery,  this  despite  the  Commission 
recommendation based on their evaluation the 2nd RBMPs. Instead, they appear to provide a general 
statement on the adequacy of the contributions and of water use sectors to cost recovery. 

The RBMPs report quantitative estimates of environmental costs, calculated at the hand of a national 
methodology of appraising ecosystem restoration expenses and cost savings. Thus, the costs cover 
three  impact  categories  of  environmental  impacts,  namely  water  pollution,  abstractions,  and 
hydromorphological impacts on watercourses. 

Unfortunately, the RBMPs do not demonstrate who incur these environmental costs, apart from a 
general assurance that the Polluter Pays Principle (PPP) has been applied in price setting. However, 
they  specify  that  the  PPP  is  applied  through  other,  non-price  instruments,  namely  mandatory 
abatement actions or investments in environmental protection equipment.  

31 

 
6. WFD recommendations 

Recommendations - Czechia should: 

1. 

Address the identified lack of compliance of achieving good status by increasing the level of ambition and 
reducing the compliance gap as much as possible until the next reporting cycle.  

In particular,  

a. 

b. 

c. 

d. 

consider that the exemption of Article 4 (4) WFD lapses in 2027 after the last prolongation (with 
the exception  of  the time  related exemption  for  reason  of natural  conditions, which may  run 
beyond 2027), making it necessary to achieve good status or verify the possible application of a 
lowering of objectives under Article 4(5) WFD.   
carefully  review  the  environmental  impact  of  large-scale  infrastructure  projects  such  as  the 
construction of canals or large-scale irrigation projects that affect surface water bodies according 
to Article 4 (7) WFD, weighing the pro’s and con’s and considering also alternatives to achieving 
the legitimate public objective, and provide all necessary justifications in the RBMPs.45  
Increase the investments and ensure adequate financing in prevention and restoration to ensure 
achievement of good status as required by the Directive, e.g. by making better use of the ‘polluter-
pays principle’, also for historic pollution, and by eliminating environmental harmful subsidies 
whilst ensuring affordable, just and implementing fair pricing mechanisms for all water users in 
line with Article 9 WFD.  
Identify  and  put  in  place  additional  measures  to  reduce  existing  persistent  environmental 
challenges  (pressures)  preventing  the  achievement  of  good status  as  those  pressures  will  be 
aggravated by climate change (pollution concentrates in times of less water availability).  

This implies, inter alia, also to:   

1. 

reduce  more  widely  and  more  profoundly  nutrient  pollution  of  water  bodies  caused  by  the  insufficient 
treatment of waste waters and by agriculture as well as aquaculture; 

2.  being a main cause for Czechia’s failure to achieve the objectives of the WFD; Czechia’s must revert the 
trend  on  nitrogen  pollution  where  the  balance  has  almost  exploded  between  2000  and  2017;  the 
programme of measures in the RBMPs should contain more specific data and measures for how to achieve 
good  status  by  2027  as  regards  nutrient  loads  from  agriculture  and  aquaculture;  measures  to  reduce 
nitrate and phosphor pollution of surface and groundwater bodies should by far be more ambitious and 
more comprehensive than so far, going beyond those already compulsory under the Nitrates Directive or 
voluntary under the Common Agricultural Policy and exceeding voluntary eco schemes for organic farming 
by including also legally binding and more stringent obligations to reduce significantly the excessive use 
of fertilizers in all sub-basins where water bodies are not achieving or at risk of not achieving a good 
ecological / chemical status due to nutrient (and particularly nitrate) pollution; Czechia must significantly 
better  control  the  use  of  fertilizers  and  pesticides  in  farming,  multiplying  resources  for  controls  and 
significantly  increase  administrative  penalties  for  a  breach  of  thresholds  under  the  Nitrates  Directive; 
measures are also needed to reduce eutrophication of lakes caused by large scale aquaculture; and 

45  Abstractions  of  waters  from  the  Danube  to  feed  irrigation  in  Czechia  should  also  be  assessed  in  cooperation  with 
competent authorities as part of the transboundary Danube River Basin Management Plan. 

32 

 
 
3. 

improve the treatment of urban wastewater including by connecting more urban and industrial wastewater 
discharges  with  sewers  and  wastewater  treatment  plants;  to  this  end  Czechia  should  spend  all 
programmed amounts for sustainable water management under cohesion and regional funds; and 

4.  adopt a legally binding standard for establishing the volume and level or rate of flow to the extent relevant 
for ecological and chemical status and ecological potential (“ecological flows”) within the meaning of Article 
8 (1) first indent (i) WFD;46 and to clearly link water permits to compliance with ecological flows; 

a. 

improve  river  continuity  to  facilitate  fish  migration  by  mapping  and  funding  concrete measures  to 
remove redundant obstacles that hamper river continuity, building fish passes and adopting all other 
measures appropriate to enhance river continuity; 

b.  adopt regulations to accelerate significantly the phasing out emissions of emissions, discharges and 
losses of priority hazardous substances; this should also include a comprehensive, ambitious and time-
bound action plan for cleaning-up historic pollution from industrial sites which continue to pollute 137 
ground water bodies in Czechia;  

c. 

increase the effectiveness of measures and controls to enforce the latest best available techniques, 
emission limit values and environmental quality standards on manufacturing companies in operation; 

d.  accelerate  the  energy  transition  by  phasing  out  of  brown  coal  (lignite)  for  heating  and  electricity 
production to steeply reduce aerial pollution which causes diffuse pollution of Czechia’s rivers and 
lakes;  

e. 

f. 

increase funding to construct and/or upgrade the 633 waste water treatment plants which are needed 
to close the gap according to Czechia’s 3rd RBMP (P 1-1; KTM1, KN28); improve otherwise the treatment 
of urban wastewater including by connecting all urban and industrial wastewater discharges to sewers 
and wastewater treatment plants;  

enhance the overall protection of water bodies linked to protected areas, on decline since  the 2nd 
RBMP, the Czech Republic should define additional environmental objectives and additional measures 
for such water bodies in view of their particular importance for the protection of these areas. 

5.  A  further  improvement  of  governance  and  a  better  coordination  between  the  different  administrative 
levels and authorities dealing with the implementation of the WFD and other related pieces of legislation. 
This also includes removing obstacles identified in the implementation of measures, such as insufficient 
administrative capacities and resources.  

Points of attention are:  

•  Strengthening synergies and coordination between the WFD, MSFD and other EU legislation (notably 

BHD) by taking adequate and coherent measures.  

• 

cooperate with neighbouring countries such that Czechia is able to consider pressures on terrestrial 
and  aquatic  ecosystems  depending  on  transboundary  rivers  when  pursuing,  in  cooperation  with 
neighbouring countries, plans to abstract waters from the Danube for irrigation purposes and/or 
plans to build a canal connecting Danube-Oder-Elbe.   

6.  Further close knowledge gaps and improve data availability, access to data, as well as data quality and 
comparability by harmonising methods and electronically collected data across river basin districts and 
marine regions, on monitoring, assessments, projections, economic assessment, etc. and make all data 
openly available through timely publication in line with the requirements of the INSPIRE, Open Data/Public 
Sector Information (PSI) Directives and the public sector High Value Datasets (Commission Implementing 

46 See also CIS Guidance Document no. 31.  

33 

 
 
Regulation (EU) 2023/138) to help eliminate the need for reporting. This implies better connecting data 
and  information  systems  of  all  administrations  involved  in  the  implementation  (also  others  than  the 
water  competent  authorities) and  make  better  use  of  the  opportunities  from  digitalisation  and  earth 
observation. 

This requires now:  

a.  adopt a legally binding standard for establishing the ecological potential of river stretches and 
lakes that are qualified as “heavily modified”; and the maps all measures needed to achieve such 
a good ecological potential, in particular for lakes considering that almost all lake water bodies in 
Czechia are “heavily modified”, (making the threshold of “good ecological potential” in practice by 
far more relevant for lakes than “good ecological status”);  

b.  monitoring of surface water bodies to determine the status of all lakes and rivers currently still 

in “unknown” chemical status (18.4% of all SWB);  

c.  monitor PFOS and PFAS in groundwater and surface water bodies; 

5.  monitor  and  contain  more  aggressively  invasive  alien  species  and  in  particular  adopts  measures  to 

constrain the spreading of North American crayfish47.   

This requires until the next RBMPs:  

a. 

b. 

conducting a more comprehensive gap assessment for diffuse pollutant loads from industry and 
manufacturing across all RBDs and link them clearly and directly to mitigation measures in the 
3rd RBMPs (as per WFD Article 11(3)(h)); to facilitate the achievement of WFD objectives; and 
increase measures to protect surface water bodies against run-off from fertilizers and pesticides, 
and promote and subsidise organic farming.   

conduct  more economic appraisals, in particular cost-effectiveness analysis, which can help to 
identify  and  prioritise  the  most  cost-effective  combinations  of  measures  to  achieve  faster 
progress towards the environmental objectives;  

c.  be transparent how different users contribute and how the Polluter-Pays-Principle is applied, in 
particular as regards the cost of cleaning up contaminated industrial sites and reducing nutrient 
and pesticide pollution; 

d.  monitoring of the quantitative status of ground waterbodies to increase the certainty of status 
assessments,  currently  being only  at  a  medium  level  of  confidence  for  a  majority  of  GWB,  in 
particular by always taking into consideration the status of related GWAAEs and GWDTEs which 
are not yet comprehensively considered in the groundwater quantitative status assessment of all 
RBDs; 

e.  monitoring of biological quality elements including in particular of macrophytes, phytobenthos, 
benthic invertebrates, and fish in lakes, and their salinity and nitrogen conditions; for rivers, include 
in  monitoring  also  of  all  general  physico-chemical  quality  elements  including  still  missing 
parameters  (e.g.:  for  rivers  the  general  physico-chemical  quality  elements,  transparency  and 
salinity  conditions;  for  lakes  biological  quality  elements,  macrophytes,  phytobenthos,  benthic 
invertebrates, and fish); and 

f.  assign all rivers to an intercalibration type where not yet done.  

47 E.g.: the release of predator fish that feast on invasive crayfish, such as eel, burbot, pike perch, catfish, chub, as well as 
dragonfly larvae, which successfully destroy juvenile crayfish; or the sterilization of males or emptying fish ponds to allow 
them to freeze during winters etc. 

34 

 
 
7.  Enhance the consideration of climate change in all its RBMPs ensuring that the actions identified under 
the new National Water Strategy are already implemented during the 3rd RBMP. Although not explicitly 
required  by  the  Directive,  failure  to  do  so  will  make  it  increasingly  difficult  to  achieve  the  Directive’s 
objective and, in some case, even lead to a deterioration of waters where progress has been achieved. 

Points of attention are:  

a.  promoting  measures  to  increase  water  efficiency  across  all  sectors  using  water,  be  it  in  the 

agricultural, the manufacturing, the energy (cooling) or the public water supply sectors;  

b.  more regularly monitoring water abstractions and their compliance with conditions;  

c.  making  water  abstractions  permits  more  flexible  to  allow  for  adapting  the  volumes  of  water 
abstractions in line with changes to the water balance; and to gradually adapt abstractions such 
that ground water bodies are no longer at risk of losing their good quantitative status;  

d.  adopting measures to reduce the sealing of soils in regions where groundwater bodies are at risk 
of  losing  a  good  quantitative  status,  and/  or  where  climate  change  predictions  suggest  that 
pressures will increase significantly to put ground water bodies at risk in the foreseeable future; 
this applies in particular for urban areas (see Czechia’s State of the Environment report on the 
increasing extent of built-up areas disrupting the ability of the landscape to retain water  and 
protect against floods);  

e.  adopting and putting into practice drought management plans in river sub-basins in particular 
where  ground  water  bodies  are  at  quantitative  risk  or  may  soon  be  at  risk  due  to  significant 
abstraction pressures;  

f. 

g. 

for agriculture exploring also climate adaptation measures other than the expansion of irrigation, 
in particular crop diversification and more sustainable soil management techniques that allow for 
a better retention of rainwater and would also help Czechia achieve its goals under the Nature 
Restoration Law; more sustainable soil management practices through organic farming could over 
time significantly reduce pressures both on surface and on groundwater bodies;  

for Czechia’s forestation policies, exploring alternatives to coniferous trees which are particularly 
vulnerable  to  temperature  fluctuations  and  exposed  to  bark  beetle  invasion,  leading  to  vast 
stretches of forest being logged and exposing soils to erosion and reducing the capacity of soils 
to absorb rainwater and recharge groundwater bodies.  

35 

 
 
SECTION B: 
FLOODS DIRECTIVE 

36 

 
 
 
7. Flood risk management under floods directive (FD) 

The Directive requires each Member State (MS) to scan its territory for flood risks, assess the potential 
adverse  consequences  of  future  floods  for  human  health,  the  environment,  cultural  heritage  and 
economic  activity,  identify  the  significant  risks,  map  the  flood  extent  and  the  potential  adverse 
consequences, and 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 three Units of Management (UoMs) in Czechia, which are the same as the Water Framework 
Directive’s River Basin Districts (RBD). Fluvial floods are considered as potentially significant sources 
of  flooding  in  Czechia.  Czechia  has  designated  243  Areas  of  Potential  Significant  Flood  Risk 
(APSFRs)48. The second PFRA states that the possible impact of climate change on the occurrence 
and intensity of floods in Czechia was assessed in the first PFRA in 2011. It is considered that there 
is still no concrete basis for a possible change in hydrological data characterizing the flood regime in 
Czechia.  

7.1 Flood hazard and risk maps 

To visualise flood hazard and risks, Czechia uses maps49 at the national level which covers the whole 
country.  The  maps distinguish  hazards  and  risks  with  low  probability  (1/500 years),  with  medium 
probability (1/100 years) and with high probability (1/5 and 1/20 years). The maps also show clearly 
flood extents as well as water depth but do not show the number of inhabitants potentially concerned 
although a methodology for determining numbers of affected inhabitants exists. Czechia derives the 
type of economic activity within flooded areas from land use. IED installations are not depicted in 
FHRMs, but there is a description in a report. FHRMs do not show the potentially affected protected 
areas identified in Annex IV(1)(i), (iii) and (v) to Directive 2000/60/EC. 

In terms of changes of contextual information (i.e. the way in which information about the maps is 
conveyed  to  the  public)  since  the  first  FHRMs,  the  portal  for  the  second  FHRMs  changed  into 
https://cds.mzp.cz/ and information from both the first and second FHRMs can be found in this portal. 

In terms of changes in methodologies used to prepare flood hazard maps and flood risk maps since 
the first FHRMs, the methodologies have not been changed. 

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

48 For the second PFRA some APSFRs have been aggregated, others have been removed. There is now a total of 135 
APSFRs. 
49 https://cds.mzp.cz/stretches/?version=2  

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7.2 Flood risk management plans 

Objectives and measures 

The FRMPs can be downloaded online50 for its three UoMs. Czechia established common objectives 
for  its  three  FRMPs,  comprised  of  a  strategic  goal,  general  objectives  and  sub-objectives.  The 
objectives – and in particular the strategic goal – refer to the reduction of adverse consequences of 
flooding.  Sub-objectives  refer  to  a  range  of  non-structural  initiatives,  including  spatial  planning, 
agricultural  management,  local  flood  planning,  and  flood  forecasting.  The  strategic  goal  refers  to 
human  health  and  a  basic  indicator  of  the  success  of  the  implementation  of  the  FRMPs  is  the 
decrease  in  the  number  of  inhabitants  at  risk.  Of  relevance,  the  third  general  objective  calls  for 
increasing  the  preparedness  of  the  population.  A  sub-objective  refers  to  actions  to  improve  flood 
forecasting and systems to warn the population. The strategic goal refers to reducing flood risks and 
increasing resilience for economic activity and infrastructure, the environment and cultural heritage. 
Czechia’s  second  FRMPs  identify  structural  and  non-structural  measures.  Czechia  has  reported 
measures  to  EIONET,  but  the  number  of  measures  in  the  FRMP  is  a  different  one.  Czechia  has 
indicated a level of priority for each measure reported to EIONET. In Czechia’s reporting, each measure 
is assigned one of three of these categories: very high, high and moderate (thus, there are no critical 
or  low  priority  measures).  The  largest  share  of  measures  is  reported  as  very  high  priority  (27 
measures,  47  %  of  the  total),  followed  by  high  priority  (25  measures,  44  %).  The  remaining  five 
measures are of moderate priority (9 % of the total), and all are protection measures in the Danube 
UoM (CZ1000). The second FRMPs also indicate the priority of their measures and the method of 
prioritisation  is  described  in  the  FRMPs.  The  FRMPs  identify  the  authorities  that  will  monitor  the 
implementation of the plan and state that national annual reports will provide monitoring results. 

The second FRMPs provide the costs of their structural measures. They also refer to the use of cost-
benefit analysis for flood prevention measures; however, the methods and results of the analyses are 
not provided in the plans. The FRMPs state that their structural measures are funded by the state 
budget,  by  river  basin  agencies  (which  are  state  enterprises),  by  other  public  sources,  including 
municipalities, and by EU funds, though the specific funds are not specified. The FRMPs moreover 
identify the amounts expected from each source. The three FRMPs include nature-based solutions 
that will regenerate natural  areas e.g. through water retention, but water retention reservoirs are 
also included in the plans. The non-structural measures include the elaboration or update of spatial 
plans and building permissions to implement restrictions in flood zones. The second FRMPs indicate 
that the  WFD’s  objectives were  considered  in the  identification  and  assessment  of measures  and 
structural measures need approval from local environmental authorities. The FRMPs cite Czechia’s 
Strategy for adapting to climate change; however, they provide little information on potential impacts 
of climate change on flooding or on measures to be taken.  

The second FRMPs provide an overview of the progress made by the first FRMPs, using indicators 
such as the population at risk of flooding. The second FRMPs also list 17 indicators to monitor their 
own  progress.  The  second  FRMPs  state  that,  for  all  the  indicators,  a  baseline  is  available  for  the 
evaluation of progress of their implementation. 

Czechia  reported  to  EIONET  the  progress  of  implementation  of  its  measures  using  the  following 
categories: In preparation: 36 measures; Ongoing (recurrent e.g. maintenance works): 22 measures; 
and  Ongoing  construction:  6  measures.  Thus,  Czechia  did  not  report  any  completed  or 

50 http://www.povis.cz/html/index.html?pzpr2_plany.htm  

38 

 
 
abandoned/interrupted measures. Most of the measures in preparation are located in the Danube 
UoM  (CZ1000,  21  measures,  which  is  58  %  of  all  measures  in  preparation).  The  remaining  15 
measures in preparation are split fairly evenly between the other two UoMs (Elbe, CZ5000 and Oder, 
CZ6000). Of the six ongoing construction measures, four are in the Elbe UoM and two are in the Oder 
UoM. Of the measures reported as ongoing, seven are in the Danube UoM, six in the Elbe UoM and 
nine  in  Oder  UoM.  All  12  preparedness  measures,  and  six  of  the  seven  prevention  measures  are 
reported as ongoing. Of the 36 measures reported as in preparation, 35 are protection measures, 
and one is a prevention measure. All six ongoing construction measures are protection measures. 

The FRMPs provide information on the phase of development of structural measures. The second 
FRMPs moreover include a review of structural measures in the first FRMPs. The second FRMPs note 
that some measures had not been implemented: the reasons include complicated or blocked property 
negotiations with landowners. In addition, in many cases where measures were not yet completed, 
there  were  delays  in  the  preparatory  or  other  phases  of  the  project,  in  some  cases  due  to 
administrative procedures such as a change in a spatial plan or unsuccessful negotiations with the 
nature protection authorities; in other cases, a measure was planned as part of a system of measures, 
or  otherwise  depended  on  the  implementation  of  other  measures,  and  the  above-mentioned 
problems and delays occurred to those other measures. The FRMPs thus provide an overview of the 
reasons why certain measures have been delayed. It should be noted that the plans do not indicate 
that any structural measures have been abandoned, though some were not implemented and are 
included in the second FRMPs. 

The  FRMPs  describe  coordination  with  the  WFD  on  measures.  Moreover,  Czechia’s  river  basin 
authorities are responsible for both WFD and FD measures and will coordinate implementation of 
FRMP and RBMP measures. In addition, the Water Planning Commission, a permanent advisory body, 
supports coordination between FRMPs and RBMPs. 

Governance 

The three FRMPs mention that coordination with neighbouring countries was carried out via work for 
the international FRMPs of the Danube, Elbe and Oder river basins. The FRMPs however do not provide 
further  detail  on  international  coordination,  except  the  FRMP  for  the  Oder  which  mentions  one 
measure that was negotiated on international basis with Poland, for the reconstruction of dykes51. 

The FRMPs provide little detail on the public consultation or on the active involvement of stakeholders, 
and  in  particular  little  detail  on  possible  private  sector  or  NGO  involvement.  While  separate 
documents list comments received from government authorities on the draft plans, together with the 
responses,  no  information  is  provided  on  possible  comments  from  the  public  or  from  private 
stakeholders. 

Climate change consideration 

Information on how Climate change considerations have been taken into account in the development 
of the Plans can be found in section 3.7.  

51 Measure HOD217501 - Olše, Karviná, Loukyn/O – reconstruction of dikes, bed drops and dredging, Oder UoM. 

39 

 
 
 
Progress identified in the second FRMPs 

Czechia’s second FRMPs identify indicators, which together with the main indicator provided in the 
first FRMPs will be used to monitor the plans as a whole. The second FRMPs state that, for all the 
indicators, a baseline is available for the evaluation of progress of their implementation. Further. the 
second FRMPs have addressed, at least partly, three recommendations on the first FRMPs: the method 
for the prioritisation of measures is provided,  cost estimates and an overall budget for structural 
measures are also included (though not for non-structural measures); and timetables for structural 
measures (though not all measures) are also provided. While most measures were reported as ‘not 
started’ in the first FRMPs, all the measures in the second FRMPs are either ongoing or in preparation. 
The second FRMPs now include nature-based solutions. The second FRMPs do refer to the updated 
Czech Climate Change Adaptation Strategy; the first FRMPs did not refer to the previous version of 
this strategy. The second FRMPs refer to work on floods within the updated strategy, though they 
provide few details. 

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

8. FD recommendations 

On the basis of the assessment performed, and in addition to the progress achieved already- Czechia should: 

• 

• 

• 

• 

present potential future impacts of climate change in the FHRMs and/or  discuss them in a related 
background document; 

provide  in  the  FHRM  more  references  to  studies  or  documents  where  further  details  on  the 
methodologies are available. This relates in particular to the indicative number of affected inhabitants; 

 consider pluvial flooding in the FHRM; 

provide details on how the FHRM was used for choosing objectives and measures in the FRMP; 

•  make the objectives of the FRMPs more specific and where possible linked to quantitative indicators 
and be timebound. An assessment of the progress made towards the achievement of the objectives 
should be included in the FRMP; 

• 

• 

• 

• 

link measures to objectives in the FRMP; 

base the likely impact of climate change in the FRMP also on future climate scenarios; 

consider insurance as a measure for adaptation to climate change; 

set out in more detail the progress of the measures in the FRMP 

40 

 
 
• 

• 

provide in the FRMP more information on potential climate impacts and any studies of these impacts. 
Measures should be considered to fill any knowledge gaps. 

provide in the FRMP detail on the public consultation and stakeholder involvement, such as the specific 
stakeholders that participated, the meetings and advisory groups convened, the comments received, 
and how they were taken into account. All relevant stakeholders should be involved in consultations, 
including the public, private sector and NGOs.  

• 

set out in the FRMP clearly the international cooperation and coordination activities carried out. 

•  where appropriate, consider in the FHRM flow velocity or the relevant water flow and the FRMP flood 

conveyance routes, as these are relevant to emergency response. 

• 

depending on the nature of the measures, subject the FRMP to a Strategic Environmental Assessment. 

41