During three cruises to the Bay of Gdansk, Baltic Sea, the fauna, porewater and bottom water were sampled at stations parallel to the shore and along a transect offshore. Diffusive porewater fluxes were calculated and related to the total net fluxes (TNF) of nutrients. The TNF comprise all nutrients that reach the bottom water from the sediment including diffusive nutrient efflux, discharge from macrozoobenthos and microbial activity. They were determined during in situ incubations using a benthic chamber lander, which is rarely done in coastal research. The lander restricts the physical influence of currents and waves on the sediments and only allows nutrient fluxes due to bioturbation by natural communities. Strong benthic-pelagic coupling in the shallow coastal zone suggested a crucial filter function for the bioturbated coastal sediments, which are separated from muddy deep sediments with little or no fauna at a depth of 50 m; in between is a small intermediate zone. While diffusive fluxes were highest at intermediate and offshore stations, TNF were highest at sandy coastal stations, where reservoirs of dissolved nutrients were small and sediments almost devoid of organic material. The greatest impact of macrofauna on sedimentary fluxes was found at stations whose communities were dominated by deep-burrowing polychaetes. The largest TNF were measured directly at the mouth of the Vistula River, where riverine food and nutrients supplies were highest. Macrofauna communities and sediment variables can thus serve as descriptive indicator to estimate the extent of the coastal filter. Finally, based on the total areal size of the different sediment types, annual efflux for the complete coastal zone of the Gdansk Bay was estimated to be 6.9 kt N, 19 kt Si, and 0.9 kt P. Compared to the muddy offshore area, which is twice as large, these amounts were similar for P and threefold higher for N and Si.

Dissolved organic matter (DOM) concentrations in sediment porewaters are often orders of magnitude higher than in the overlying water column resulting in a diffusive flux of DOM from sediments. The intensity and fate of this DOM flux is poorly understood. The Gulf of Gdansk in the Southern Baltic Sea is dominated by the Vistula River, one of the largest and most anthropogenically impacted rivers in the Baltic Sea catchment. The sediment characteristics of the region are varied, from mixed sandy conditions near shore to mud sediments in the Gdansk Deep. We investigated the significance of sediment‐derived DOM in the Gulf of Gdansk in comparison to that supplied by the river. Sediment‐derived DOM in the region was found to have an organic matter fluorescence signature distinct from the DOM in the water column. The visible wavelength fluorescence could be used to distinguish organic matter from near shore sediments influenced by riverine sources and organic matter from deeper offshore sediments, influenced by more pelagic sources. Ultraviolet‐A wavelength fluorescence dominated the sediment flux but was rapidly removed in bottom waters suggesting that it may contribute to bottom water oxygen consumption. While there is potential for DOM fluxes from sediments in the Gulf of Gdansk, the high background pelagic concentration of DOM in these waters and the much stronger influence of the Vistula River can mask the contributions from sediments.

The impact of synoptic scale and mesoscale variability on the Lagrangian residence time (LRT) of the surface water in the Bay of Gdańsk was investigated using the results from an eddy-resolving model. The computed LRT of 53-60 days was up to four times longer than the estimated flushing time reported by Witek et al. (2003). The highest residence times were those of Puck Bay and near the coast, shallower than 50 m water depth, especially during the winter. These sites also had the highest annual mean in LRT. During the summer, when the level of biological activity is high, the LRT distribution was very heterogeneous and patchy, possibly due to the dynamics of varying eddy field and to variable wind forcing. Long-term run tracking of the inflowing water from the Vistula River (VR) showed a broad spectrum of tracer distribution. The potential impact of a much higher LRT on the near-coastal nitrogen cycle, coastal filter function and genetic differentiation is discussed, and the consequences for coastal zone management are considered. Since residence time is the most important factor regulating nutrient cycling, the incorporation of residence time into the Marine Strategy Framework Directive descriptors would result in an improved, unbiased evaluation of good environmental status.

To better understand food webs and the trophic relationships of marine animals studied by means of preserved material requires knowledge of the effects of preservation on the organic materials of interest. We examined the effects of formalin and ethanol preservation on the stable isotope values of carbon and nitrogen in the bivalves Mya arenaria and Tellina fabula and in the polychaetes Magelona spp. and Hediste diversicolor. Samples of these organisms were collected in the southern North Sea and the southern Baltic Sea, and were preserved with formalin, ethanol, and by freezing. The stable isotope patterns of carbon and nitrogen in the chemically preserved samples were related to those in the frozen samples. The influence of different preservation methods on the stable isotope composition was analyzed using a correction model that is independent of the molar C:N ratio. For most samples from the North Sea, significant correction factors were obtained. In contrast, none of the samples from the Baltic Sea were impacted by the preservatives with respect to their δ 15 N values, and, for H. diversicolor, also with respect to the δ 13 C values. In these cases, corrections of the δ 13 C and the δ 15 N values were not necessary. Quantitative metrics using a phenotype-based approach were computed to characterize aspects of the trophic structure of the benthic community. Phenotypic clustering in isotopic diversity indicates no competition for food between the dominant species. Our results indicate that a representative dominant mollusk and polychaete species have a higher trophic position in the Baltic Sea than in the North Sea.