Eutrophication and climate change, key environmental concerns, are both linked to the carbon and nitrogen cycles hence the improved understanding of these cycles is essential. Currently, there is no system that simultaneously measures the fluxes of the three key gas phase products of nitrogen and carbon cycling (CO2, CH4 and N2O) in submerged ecosystems with hourly time resolution. A “Lake-in-a-box” (mesocosm) was developed in the laboratory which allowed the monitoring of key components of the carbon and nitrogen cycles within the air, water and sediments. The approach is automated, simple and time efficient and novel in its ability to examine many different carbon and nitrogen compounds in all three physical component of the “lake”. Dramatic fluctuations in gaseous flux and the concentrations of overlying water and sedimentary carbon and nitrogen compounds were noted over a three week period. These were split into five distinct phases which were linked to changes in sedimentary N and C cycling. The results highlighted the important of links between the two cycles and supported recent studies showing that estuarine sediments can act as both a source and a sink of nitrogen.