Comparisons among three Hamilton City streams indicate that the Mangakotukutuku has higher mean dissolved oxygen levels, and concentrations of dissolved and total organic carbon, compared to the Kirikiriroa and Waitawhiriwhiri (Williamson (2001; Appendix 1). Most of the biochemical oxygen demand is thought to originate in rural parts of the catchment. pH, a measure of acidity, was near neutral (averaged around 6.9) in the Mangakotukutuku, and simliar to that  in the Waitawhiriwhiri or Kirikiriroa. An analysis of trends up to 2002 indicated significant declines over time in pH at Peacockes Rd, indicating that the water is getting more acid (Vant & Smith 2004; see also Beard 2011).

The Mangakotukutuku has higher total phosphorus concentrations compared to the Kirikiriroa and Waitawhiriwhiri (Williamson 2001; Appendix 1). Around 70% of total annual phosphorus and over 90% of total nitrogen exported annually are estimated to be derived from rural parts of the Mangakotukutuku catchment (Hickey et al. 2001), although the rural contribution does not appear to have been quantified directly. An analysis of trends up to 2002 indicates significant increases in total nitrogen and phosphorus concentrations in this catchment (Vant & Smith 2004). Regionally, total nitrogen and phosphorus concentrations have increased faster in catchments with higher proportions of pasture. Levels of ammonia, a form of nitrogen that is toxic to fish, are considerably less in the Mangakotukutuku (median = c .0.25 g NH₄-N m^-3) compared to the Waitawhiriwhiri and Kirikiriroa (Williamson 2001).

Most (70%) of suspended sediment carried by the Mangakotukutuku  is estimated to be derived from rural areas in the catchment. In the upper reaches, humic substances from peat soils colour the water (Williamson 2001), whereas further downstream turbidity appears to be derived from particles of suspended silt. Wilding (1998) reported lower average turbidity levels in the Mangakotukutuku (c. 27 NTU) than in the Waitawhiriwhiri (c. 33 NTU) and Kirikiriroa (c. 43 NTU). However, the Mangakotukutuku had higher average turbidity levels than several smaller Hamilton urban streams (Appendix 2 of Wilding 1998). The level of  turbidity in the Mangaotukutuku is high enough to disrupt feeding and movement of some native fish.

By far most of the lead, zinc and cadmium carried by Mangakotukutuku Stream is estimated to be derived from urban parts of the catchment (Hickey et al. 2001). Mass loads of these metals were 4^th to 5^th highest of 15 Hamilton City catchments investigated, although considerably less than the industrialised Waitawhiriwhiri and Te Rapa catchments. Despite these differences in likely heavy metal loads, average conductivities of 200 to 230 mS.cm^-1 reported by Wilding (1998; Appendix 2) were similar in these three streams and considerably less than in some smaller Hamilton urban streams. Conductivity is often used to indicate the concentration of dissolved ions present in water.

Contamination by faecal bacteria was considered a major “stressor” in the Mangakotukutuku  by Williamson (2001), presumably because of its effects on human health rather than for ecological reasons because these bacteria do not adversely affect aquatic life. Mean numbers of faecal coliforms are considerably less in the Mangakotukutuku compared to the Waitawhiriwhiri, but slightly higher than in the Kirikiriroa. Most faecal coliforms carried by the Mangakotukutuku appear to be derived from upstream rural parts of the catchment, whereas around half of the E. coli is estimated to be derived from urban sources (Hickey et al. 2001). A synoptic survey carried out on 22 January 1998 indicated low levels of bacteria, ammonia and turbidity in the Peacockes branch compared to the main stream in Sandford Park (Williamson 2001; Appendix 3).