In recent years the Ōtūkaikino River catchment has had some of best water quality and stream health of all Christchurch rivers. However, the absence of stoneflies from macroinvertebrate surveys in 2017 indicates that all may not be well with the catchment. Given stoneflies are typically associated with high habitat and water quality, their decline or disappearance may signal stream health challenges that require further attention. A 12-month monitoring programme was created for the Ōtūkaikino River catchment to determine potential sources of pollution and habitat limitation related to this apparent decline. A range of physical, chemical and biological parameters were investigated across ten sites in the catchment in 2019 and 2020. The moderately pollution sensitive cased caddisfly Pycnocentria was a dominating taxon at many sites, though pollution tolerant Potamopurgus snails and pollution sensitive Deleatidium mayflies were also typically in high numbers. Four Zelandobius stoneflies were identified in catchment monitoring surveys in 2019, indicating that the catchment is still able to support populations of stoneflies, despite the apparent decline between 2008 and 2017. Metrics for ecological health generally increased downstream towards the middle reaches. Site scores ranged from poor ecological health (upper Waimakariri South Branch) to excellent (middle reaches). This differed to the generally good-excellent ecological health reported in 2017. Low concentrations of trace elements suggested they were generally not a key contributor to changes in ecosystem health in the Ōtūkaikino River catchment. Key exceptions were dissolved arsenic, chromium, copper and zinc at some sites. In sediment, metal concentrations were generally low, except for two headwater sites of the Waimakariri South Branch. These two sites recorded high levels of most parameters analysed, with lead and copper exceeding ANZECC (2000) interim sediment quality guidelines. Most other water quality parameters were within ANZECC (2000) water quality guidelines for ecosystem protection, with a few key exceptions. Dissolved oxygen reached low concentrations at several sites. Elevated levels of faecal coliforms were recorded in some samples, though E. coli was comparatively low. While nitrate-nitrogen concentrations were low, DRP (dissolved reactive phosphorus) was consistently elevated above ANZECC (2000) water quality guidelines at one site, as was ammoniacal nitrogen at several sites. The main factors identified in this study that contributed to this variation in macroinvertebrate community health and water quality were differences in riparian and canopy cover. They were typically highest in the middle reaches, though there were some other areas of thick vegetation. In particular, much of the upper reaches had limited mature shading plants and sediment filtering plants. Localised inputs, such as trace elements in two Waimakariri South Branch sites, were also potential contributors. Substantial planting efforts have occurred in the catchment in the last couple of decades. This study recommends that these efforts continue, with a focus on intercepting sediment and shading the waterway. Further monitoring and research in the vicinity of the two sites where high levels of trace elements were recorded is also recommended.