Information and communication technology are crucial enablers of networked organizations, but effective Cooperative Information Systems remain difficult to design because there are no tools to assess their short- term operational effectiveness and long-term impact on organizational knowledge. We present three contributions toward a solution of these problems: 1) we identify information flow categories as a crucial conceptual abstraction; (2) we show how successful simulation models for long-term analysis of team performance can be extended to include the crucial problems of cross-unit information management and exception handling; (3) we exploit recent results on multi-simulation to enable an integration of these long- term models with queuing-type simulation models usually applied in operational business process analysis. The approach has been implemented in an interactive analysis environment called MultiSim, and has been tested in a case study in the production industry.