The increment in water pollution due to the massive development in the industrial sector is a worldwide concern due to its impact on the environment and human health. Therefore, the development of new and sustainable alternatives for water remediation is needed. In this context, aerogels present high porosity, low density, and a remarkable adsorption capacity, making them candidates for remediation applications demonstrating high efficiency in removing pollutants from the air, soil, and water. Specifically, polymer-based aerogels could be modified in their high surface area to integrate functional groups, decrease their hydrophilicity, or increase their lipophilicity, among other variations, expanding and enhancing their efficiency as adsorbents for the removal of various pollutants in water. The aerogels based on natural polymers such as cellulose, chitosan, or alginate processed by different techniques presented high adsorption capacities, efficacy in oil/water separation and dye removal, and excellent recyclability after several cycles. Although there are different reviews based on aerogels, this work gives an overview of just the natural biopolymers employed to elaborate aerogels as an eco-friendly and renewable alternative. In addition, here we show the synthesis methods and applications in water cleaning from pollutants such as dyes, oil, and pharmaceuticals, providing novel information for the future development of biopolymeric-based aerogel.