You've asked a very broad question! Many fisheries are managed based on keeping exploitation levels below benchmarks and biomass above targets. The benchmarks and targets are developed through statistical modeling methods which vary depending upon available data. Monitoring direct impacts might include annual landings and sale of fish, total capture estimates, and year to year monitoring and estimation of exploitation levels and biomass. Indirect measures of direct impact might include survey indices. Monitoring indirect impacts (habitat loss, ecosystem function) is more complex. Typically some sort of indicator species might be chosen, or the areal coverage of a fishery estimated.
These topics are current, and some techniques are underdevelopment or revision.
More help will likely follow if you can narrow the range of your question or provide greater detail about it.
There's a huge literature on this subject! Try Google Scholar. Nonetheless, here a couple references to get you started:
Hughes, K. M., Kaiser, M. J., Jennings, S., Mcconnaughey, R. A., Pitcher, R., Hilborn, R., Amoroso, R. O., Collie, J., Hiddink, J. G., Parma, A. M. and Rijnsdorp, A. (2014)
Investigating the effects of mobile bottom fishing on benthic biota: a systematic review protocol. Environmental Evidence. 3:23 doi:10.1186/2047-2382-3-23
Lambert, G. I., Jennings, S., Kaiser, M. J., Davies, T. W. and Hiddink, J. G. (2014)
Quantifying recovery rates and resilience of seabed habitats impacted by bottom fishing. Journal of Applied Ecology, 51, 1326-1336.
de Marignac, J., J. Hyland, J. Lindholm, D. Kline, and L. Balthis. 2009. A comparison of seafloor habitats and associated benthic fauna in areas open and closed to bottom trawling along the Central California continental shelf. Marine Sanctuaries Conservation Series ONMS-09-02. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, Office of National Marine Sanctuaries, Silver Spring, MD. 44 pp.
It'd be better if you specified more details on the background of your question.
As far as as I can understand, you need to find out what happens to the marine environment where the bottom (I assume) is trawled. You need to start with description of the bottom character, for each type of bottom would be differently affected. Then comes the description of the fishing gear employed, for each type of trawling gear differently affects the bottom. The first and perhaps the only parameters that can be IMO quantified are the frequency at which each spot of the bottom is passed by a trawl during a given period and, consequently, the spans of time when the bottom can "rest". Next comes the real complexity: the biota in the trawled area, starting with micro-benthos and ending with top predators, especially how the removal of some of it affects the rest. Still another factor, which may affect the environment is the dead and living by-catch jettisoned by the trawlers. I'd say that one must assume a specific qualitative approach to each individual habitat. For some, very non-dynamic habitats where the above factors don't change or their changes can be reliably quantified, a mathematical model may just be valid. MB-Y
Hi Olalekan, forgot to mention climatic and hydrographic factors that may quite a strong role over shallow bottom, where even weather may cause and control currents down to the bottom. There, on soft and sandy grounds, strong current may fast "sweep away" all traces left by trawl gear. MB-Y
We have recently conducted an assessment of bottom fishing gears (longline and trawl) in the deep sea fisheries in the Australian EEZ in the Southern Ocean, and developed a generic method for assessing the level of disturbance by anthropogenic activity in a seascape, combining effort data, habitat mapping and video of fishing gear behaviour. This report and the references therein may help you frame your project: http://www.antarctica.gov.au/__data/assets/pdf_file/0010/142849/FRDC-Final-Report-2014.pdf