Water quality at four coal mines in southern New Zealand can be related directly or indirectly to the geology and mineralogy of the stratigraphic sequence in which the coal mines occur. The Late Cretaceous Taratu Formation of the Kaitangata coalfield formed in a marginal marine setting during regional marine transgression, and marine incursions punctuated coal formation. Abundant authigenic and remobilised pyrite at the Wangaloa mine (typically 4 wt%S in coal) in the Kaitangata coalfield has oxidised and caused acidification of mine waste rocks (to pH 1) and mine waters (to pH 3). Similar or even greater amounts of pyrite occur locally at the nearby Kai Point mine, although the mined seam typically has <2 wt%S. However, dissolution of carbonate concretions in marine sediments immediately overlying the mined seam at Kai Point mine ensures that acid generated by pyrite oxidation is neutralised, and the site generally has substrates and waters with near‐neutral or alkaline pH. The close stratigraphic association between coal and marine sediments at Kai Point mine has resulted in high B contents in coal (up to 500 mg/kg) about 10 times higher than at the nearby Wangaloa mine. Both mines have elevated dissolved B contents in mine waters (up to 6 mg/L at Wangaloa). The Late Cretaceous coal‐bearing sequence at Ohai is entirely nonmarine, pyrite is rare or absent, and no environmental acidification occurs. Likewise, the Miocene coal‐bearing strata at Newvale coal mine have negligible pyrite and no acidification occurs from these rocks. However, iron sulfide cements have formed in Pliocene gravels from groundwater derived from rain with marine aerosols. Oxidation of this sulfide material has caused localised acidification at Newvale mine. Acidification has caused localised and generally short‐term elevation of dissolved trace elements at Wangaloa and Newvale mines, with dissolved Al up to c. 2.5 mg/L at Newvale. Suspensions of clay minerals cause turbidity at all mines. Well‐washed, coarse (>1 μm), detrital kaolinite at Kai Point, Wangaloa, and Newvale mines settles readily (within days). Chlorite from disaggregated labile clasts in overlying Pliocene gravels dominates longer term turbidity at Newvale, but the turbidity decreases rapidly on a time‐scale of months. Fine‐grained (including sub‐micrometre) poorly sorted authigenic kaolinite from labile clasts in the coal‐bearing strata at Ohai causes long‐term turbidity, with negligible setting over 9 months. The stratigraphically controlled processes quantified in this study can be used to predict the nature and scale of potential water quality changes in new coal mines in southern New Zealand.