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Eelgrass depth limits and water clarity in the Skive Fjord estuarine system have not improved despite nutrient input reductions of 30%. Long-term monitoring data (1989–2010) were used to investigate the underlying causes. Dissolved inorganic and organic nitrogen concentrations decreased significantly over time, whereas particulate organic nitrogen concentration, assumed to consist primarily of phytoplankton and phytoplankton detritus and calculated as a proportional factor to chlorophyll a, did not change. Total organic carbon, mostly of autochthonous origin, remained constant despite reduced nitrogen concentrations, resulting in an increasing C:N ratio of the organic material in the water column. Phytoplankton primary production also remained constant suggesting that phytoplankton growth was only limited by nitrogen to a minor degree. Alleviated grazing pressure caused by a reduction in the blue mussel standing stock and a pelagic food web dominated by jellyfish may have contributed to the constantly high phytoplankton levels. Particulate inorganic matter, likely reflecting sediment resuspension, increased over time, most probably in response to removal of blue mussels and declining eelgrass cover. The Skive Fjord estuarine system is affected by multiple pressures—nutrient enrichment, mussel dredging and climate change that must be addressed together for water clarity to improve and eelgrass to recover.

In Denmark, as in many other European countries, the diffuse losses of nitrogen (N) and phosphorus (P) from the rural landscape are the major causes of surface water eutrophication and groundwater pollution. The export of total N and total P from the Gjern river basin amounted to 18.2 kg ha−1 and 0.63 kg P ha−1 during June 1994 to May 1995. Diffuse losses of N and P from agricultural areas were the main nutrient source in the river basin contributing 76% and 51%, respectively, of the total export. Investigations of nutrient cycling in the Gjern river basin have revealed the importance of permanent nutrient sinks (denitrification and overbank sedimentation) and temporary nutrient storage in watercourses. Temporary retention of N and P in the watercourses thus amounted to 7.2–16.1 g N m−2 yr−1 and 3.7–8.3 g P m−2 yr−1 during low-flow periods. Deposition of P on temporarily flooded riparian areas amounted from 0.16 to 6.50 g P m−2 during single irrigation and overbank flood events, whereas denitrification of nitrate amounted on average to 7.96 kg N yr−1 per running metre watercourse in a minerotrophic fen and 1.53 kg N yr−1 per linear metre watercourse in a wet meadow. On average, annual retention of N and P in 18 Danish shallow lakes amounted to 32.5 g N m−2 yr−1 and 0.30 g P m−2 yr−1, respectively, during the period 1989–1995. The results indicate that permanent nutrient sinks and temporary nutrient storage in river systems represent an important component of river basin nutrient budgets. Model estimates of the natural retention potential of the Gjern river basin revealed an increase from 38.8 to 81.4 tonnes yr−1 and that P-retention increased from −0.80 to 0.90 tonnes yr−1 following restoration of the water courses, riparian areas and a shallow lake. Catchment management measures such as nature restoration at the river basin scale can thus help to combat diffuse nutrient pollution.

The mass balance for total nitrogen (N) was studied over a four-year period in 16 shallow mainly eutrophic 1st order Danish lakes. Water was sampled in the main inlet of each lake 18–26 times annually, and from the outlets and the lake 19 times annually. Water was also sampled from minor inlets, although less frequently. N input and output were calculated using daily data on discharge (Q), the latter being obtained either from the Q/H relationship based on automatic recordings of water level (H) for the main in- and outlet, or by means of Q/Q relationships for the minor inlets. Annual mean N retention in the lakes ranged from 47 to 234 mg N m−2 d−1, and was particularly high in lakes with high N loading. Annual percentage retention (N ret −y%) ranged from 11 to 72%. Non-linear regression analysis revealed that hydraulic retention time and mean depth accounted for 75% of the variation in annual mean N ret −y% and, in combination with inlet N concentration, accounted for 84% of the variation in the in-lake N concentration. N ret % varied according to season, being higher in the second and third quarter than in the first and fourth quarter (median 18–19%). A simple model was developed for predicting monthly nitrogen retention (N ret −m) on the basis of external N loading, the lake water pool of nitrogen N pool , hydraulic loading and lake water temperature. Calibration of only two parameters on data from the randomly selected 8 out of 16 lakes rendered the model capable of accurately simulating seasonal dynamics of the in-lake N concentration and N ret −m in all 16 lakes. We conclude that with regard to shallow, eutrophic lakes with a relatively low hydraulic retention time, it is now possible to determine not only annual mean nitrogen retention, but also the seasonal variation in N ret−m . Prediction of seasonal variation in N loading of downstream N-limited coastal areas is thereby rendered much more reliable.

We review various aspects of the structure and functioning of Danish estuaries from data collected by the National Monitoring Program and from information in published sources. We present data on the physical, chemical, and biological characteristics of estuaries in Denmark, we evaluate the functioning of these systems as filters and transformers of nutrients and we evaluate the outlook for Danish estuaries in the future. Danish estuarine systems are for the most part shallow (