There is substantial evidence that climate warming affects terrestrial and marine ecosystems. In addition to the geographic shifts of marine species and communities, comprehensive mesocosm experiments provide insight in the behavior of species and simplified ecosystems under climate warming conditions. Food web dynamics and stability has been topical in contemporary ecology, and while these aspects receive considerable attention, few studies have quantitatively examined the impact of climate warming on complex marine ecosystems and their food webs. Here we examine the response of a large marine ecosystem, the Sylt-Rømø Bight in the northern German Wadden Sea, to warmer temperatures by means of ecological network analysis (ENA). Three quantitative network models (of 67 model compartments each) were constructed for each of 4 non-consecutive years (1995, 2007, 2011, 2013). A base-line model at the mean annual ambient temperature, and models at +3 °C and +5 °C above the annual mean were constructed for each year (a total of 12 models) and assessed by ENA protocols. Results showed i.a. an intensification of detrital production and consumption, substantial increase in the total system throughput (TSTP), decline in consumption of phytoplankton and macrophytes, an increase in the total overhead, an increase in community respiration, and an increase in the system's P/B and R/B ratios. The mean relative ascendency declined compared to the base models by 2.35% and 2.28% in the +3 °C and +5 °C networks models respectively. It is clear from the suite of system metrics and ratios that the ecosystem becomes less organized, more dissipative and shifts towards detritus based food webs at higher water temperatures.