This paper analyzes how an agent-based simulation model of Stockholm can be used for water transitplanning. A new route for commuters by boat was added to the model of Stockholm’s existingtransport system and evaluated. By comparing results from the model and statistic data fromTrafikförvaltningen Region Stockholm during the morning rush-hour, a scale factor was calculated.The scale factor was later used to adjust the number of travelers on the added new water transit routeas the model underestimate the number of persons who use the available public transport by boat. Thelarge size of the calculated factor made the results uncertain when trying to predict any effects the newroute would have, e.g. on congestion in the system. Simulations of the new transit line resulted in amajority of short trips, between stations were the other public transit options took longer routes. Thetransit stops close to the city centre were used the most and most trips were conducted between them.To gain an improved ability to simulate water transit, continued studies of people’s preferencesregarding mode choice appear to be crucial.