We consider the problem of parameter estimation and output estimation for systems in a transmission control protocol (TCP) based network environment. As a result of networked-induced time delays and packet loss, the input and output data are inevitably subject to randomly missing data. Based on the available incomplete data, we first model the input and output missing data as two separate Bernoulli processes characterised by probabilities of missing data, then a missing output estimator is designed, and finally we develop a recursive algorithm for parameter estimation by modifying the Kalman filter-based algorithm. Under the stochastic framework, convergence properties of both the parameter estimation and output estimation are established. Simulation results illustrate the effectiveness of the proposed algorithms.