Chile has a relatively long history of monitoring and managing large-scale commercial fish stocks. However, many other small-scale fisheries, particularly those operating in estuaries, usually lack basic fisheries and biological information. International experience indicates that a monitoring system designed for large-scale stocks cannot simply be resized to address the complexity, relatively low total economic value, and the large number of actors and supply chains in small-scale fisheries. This article proposes a strategy to monitor data-poor fisheries operating in estuaries. The striped mullet (Mugil cephalus), locally known as “lisa”, in the Rapel River, central Chile, was selected to establish a pilot monitoring program for small-scale fish resources. From May 2022 to May 2023, fisheries information, including fleet description, catch and effort data, and fish biological attributes such as length and weight, were collected and described for the first time in the region. Drawing insights from this case study, we propose developing a generic monitoring system tailored specifically for monitoring fish stocks in estuaries. This conceptualization is based on: i) change agents, who are individuals trained to work with both the social and biological dimensions of each coastal fish stock; ii) experienced fisheries scientists outside government agencies; and iii) local fishers' knowledge to provide constant feedback for adapting temporal and spatial scales for monitoring. This monitoring scheme is cost-effective and can be efficiently replicated in other estuarine fisheries in Chile.