Bayesian recursive estimation is used to analyze performance parameters of a membrane separation system based on historical operational data of a membrane system. Bayesian estimation considers historical data over prior time intervals to predict future membrane separation performance to avoid unexpected downtime and unanticipated maintenance. A set of state variables used for modeling performance is used with a degradation model of to anticipate performance changes and maintenance based on measured properties of permeate, non-permeate, and feed flows.