Bottom trawling is a type of fishing in which a net, or other collection device, is dragged over the seabed to catch demersal fish, crustaceans and shellfish. In this thesis, I examined the effects of bottom trawling on the benthic ecosystem. I showed that trawl fishing may reduce benthic diversity and change the functional composition of the benthic community. These negative effects are habitat specific and may affect the food availability of fish that feed on part of the benthos. Using a modelling approach, I found that the negative effects of trawling (mortality) on benthos may both result in a positive or negative effect on the production of target fish and fisheries yield. This highlights that to successfully manage an area subject to trawl fisheries, such as the North Sea, it is imperative to understand how the food web that the benthos and the fish are part of, functions.