Kotwicki has worked in the Groundfish Assessment Program (GAP) in the Resource Assessment and Conservation Engineering Division in the Alaska Fisheries Science Center since 2001. Presently he manages GAP activities and performs research to improve fisheries-independent survey data products for fisheries assessment and management advice. GAP's main task is to conduct bottom trawl surveys to assess the condition of groundfish and shellfish stocks in Alaskan marine waters. GAP's role is to plan, execute, analyze, and report results from the surveys to establish time series estimates of the distribution and abundance of Alaska groundfish resources in the Gulf of Alaska, Bering Sea Shelf, Bering Sea Slope, and Aleutian Islands. GAP work also involves taking part in the fisheries stock assessment process by providing survey derived population estimates for stock assessment models, collecting data necessary to obtain ecosystem indicators, and performing research relevant to Alaska fisheries.

Kotwicki's research focuses on improving methods to estimate abundance of fish stocks from data collected during bottom trawl and acoustic surveys. He also performs research on estimating survey gear selectivity and catchability, and evaluating the effect of environment on fish distribution and seasonal migrations.

Kotwicki received his MSc from the University of Gdansk (Poland) and PhD from the University of Washington (Seattle). His MSc focused on the ecology of macrozoobenthos in the Baltic Sea and his PhD focused on developing methods to improve estimates of abundance and distribution of semipelagic species by combining acoustic-trawl and bottom-trawl survey methods.