**1. Introduction**

Of all the water on earth, freshwater accounts forjust 0.01% and covers only 0.8% of the planet's surface [1]. Freshwaters are among the most threatened ecosystems of the world, and thus, understanding their health statuses is of special relevance. Indeed, the physical, chemical, and biological integrities of water are highly importantfor successfully implementing conservation and management strategies before ecosystem health or biotic integrity are affected [2–4]. This chapter provides a review of known biotic integrity indicators, including benthic macroinvertebrate and fish communities that have been proposed to serve as water quality indicators. In addition, the pros and cons of using aquatic communities as water quality indicators are discussed. Finally, we present a research case study in which benthic macroinvertebrate and fish communities are used as bioindicators, in addition to discussing the effectiveness of using illustrative examples for streams subject to several agriculture uses in a region of Chile dominated by agricultural activities.

Worldwide, a primary threat to freshwater ecosystems is the rapid changes occurring in land uses (**Figure 1**), a situation that has intensified over the past decade [5, 6]. Most recent land use conversion has been for crop production, which notably impacts proximal ecosystems due to changes over extensive crop areas [7]. In particular, the fertilizers and pesticides used in agriculture negatively affect freshwater ecosystems by draining into rivers, where eutrophication and other negative effects, such as high sediment deposits and postsedimentation, subsequently occur. Furthermore, the extensive land use of farming many times results in landscape deforestation, which often arrives to the riverbank itself. This deforestation can increase the temperature of and quantity of light in river water. When coupled with eutrophication, the trophic changes within the aquatic ecosystem can be disturbed, causing, for example, a decreased quantity of aquatic taxa as compared to rivers with fewer alterations [8, 9].

**Figure 1.** Examples of land use in the central-south of Chile. Left: Stream nearby corn crops, right: Stream borderer by native forest of the Maule Region watershed (photographs by P. Fierro).
