The use of modeling and estimation strategies appears as a valuable tool to increase the efficiency of the open channel irrigation systems (OCIS). This paper is focused on exploring the feasibility, advantages, and conditions in the implementation of a moving horizon estimation (MHE) approach designed from an approximated model that contemplates mass and energy balances of the channels, which is useful to differentiate when a change of level is a conduction change effect, or when the change is due to an unknown input. The estimation strategy is evaluated via simulation using a test case reported in the literature. The results show that, with the use of the proposed estimation strategy, it is possible to reach an optimal estimation of the total amount of unknown inputs.