Coupled change in land and water use due to increased farming intensity is a main factor affecting water quality and quantity, ecological functions and biodiversity globally. Prolonging growing seasons and increasing productivity in wetlands through irrigation have been targeted for increasing food security, particularly in developing countries. Nevertheless, irrigation and drainage have often been associated with degradation of water quality through increased agrochemical and fertiliser runoff and leaching at local scales. In this study, we investigated water quality in streams used for irrigation in a wetland area in Kilombero Valley, Tanzania. We measured physical-chemical water parameters and collected macroinvertebrates with different sensitivity to water quality across several small irrigation schemes covering various conditions. Turbidity, temperature, nitrate-N, and ammonium-N were significantly higher at sampling sites downstream of irrigation compared to upstream. Macroinvertebrate diversity, richness and average score per taxa (ASPT) were higher in general in sampling sites upstream of irrigation, with more sensitive macroinvertebrates decreasing in abundance downstream. There was a positive correlation between physical-chemical parameters and macroinvertebrate indices across the sites. We demonstrate that macroinvertebrate indices can be used as a quick assessment of water quality in response to irrigation schemes in small-scale farming systems of Tanzania. This in turn can allow us to track changes affecting wetland ecosystem function and biodiversity at higher trophic levels and across larger scales, thereby providing useful early warnings to help avoid widespread degradation under widespread agricultural intensification.Water 2019, 11, 671 2 of 22 extent and magnitude of impacts of anthropogenic activity at small scales to support management decisions and avoid compounded impacts at larger scales.Usually, the main source of agricultural irrigation water in wet landscape environments comes from surface water. Because of spatial variation of water chemistry in wetlands, streams and rivers, assessment and monitoring programs are necessary to provide robust insights into the quality and quantity of surface water supplies [11][12][13]. Increased use of chemicals and excess draining of wetlands for agriculture and the associated irrigation can have impacts not only on aquatic ecosystem, but also on human health. Fertilisers and agrochemicals impact physical-chemical characteristics of surface water and biota at different spatial scales [7,14]. Excess nitrate-N in drinking water, for example, impacts young livestock, pregnant women and infants on a local scale [15]. Ammonia and phosphorous in excess cause unpleasant colour, taste and odour of water [6]. At larger scales, leaching of excess nutrients can cause overproduction, algal accumulation and decrease dissolved oxygen in aquatic and wetland environments [16,17]. When pollution goes beyond the self-purifying ability of wetland ecosystems, death of aqu...