Massive portions of a ~ 300 °C black smoker (Finn) and a diffusely venting, intermediate temperature (~ 200 °C) chimney (Roane) recovered from the Mothra Hydrothermal Field on the Juan de Fuca Ridge have been analyzed in detail for bulk chemistry. The size of the recovered pieces of chimney enabled physical segregation and analysis of distinct chemical zonation within the structures. In particular, large variations in the concentrations of minor and trace elements in the different mineralogical zones provide new insight into the processes involved in chimney growth that are not evident from the bulk mineralogy. Systematic zonation of trace and minor elements is strongly influenced by redox conditions, multiple host phases, single or dual fluid source, and the mixing–cooling history of the fluids, even within an individual mineralogical zone. Distinct chemical microenvironments within the chimneys are recognized that provide a basis for detailed reconstruction of the changing conditions in the interiors of the chimneys during their growth. In Finn, 14 discrete chemical microenvironments are recognized in 80 of 90 samples based on high resolution zoning of major and trace elements. Four of the microenvironments are Cu-rich, three are Zn-rich, one is Fe-rich with low Cu, two are Ca-rich, three are SiO 2-rich, and one is Ba and SiO 2-rich. In Roane, 24 discrete chemical microenvironments are recognized. Six of the microenvironments are SiO 2-poor (< 1 wt.%) with low SO 4, two have low SiO 2 (1–10 wt.%) and low SO 4, four have low SiO 2 and are SO 4-free, four have moderate SiO 2, three are SiO 2-rich, four have low to moderate Ba, and one is Ba-rich. The trace elements Se, Co, In, and Te do not display their typical simple associations with high concentrations of Cu. Variable Se concentrations in the most Cu-rich samples likely reflect variable Se/S ratios of the hydrothermal fluids in response to changing pH, oxidation state or mixing. Co and Te are strongly partitioned into pyrite instead of chalcopyrite indicated by concentrations of these elements remaining high even as the Cu content decreases. Indium also may be present either in chalcopyrite or in Zn sulfides ± chalcopyrite disease. In Roane, an unexpected correlation between Zn, Cd, Cu and Se is thought to reflect buffering of the fluids to a high pH by ammonia, which increases the saturation temperature of Zn sulfides and caused codeposition of Cu and Zn, with Cd enriched in Zn sulfides and Se enriched in Cu sulfides. The notable Ag enrichment in the Cu-rich samples from Finn are distinct from East Pacific Rise black smokers, possibly due to the lower temperatures (~ 300 °C vs. ≥ 350 °C) and higher fluid pH. Lower temperature assemblages in both Finn and Roane are enriched in Sb, Tl, Hg, Pb, ± Au, and ± Ag. Arsenic is enriched in some low-temperature zones but is most strongly correlated with Mo in pyrite; both elements are also absorbed from seawater as oxyanions. Uranium and V are also interpreted to have a seawater source and both may be present in clay minerals, together with the alkalies (Na, K, Rb, and Cs) while U may also be associated with sulfate minerals. Variable enrichments of Al 2O 3, U, and V in the silica-rich microenvironments within Finn and Roane indicate either seawater–hydrothermal fluid mixing or conductive cooling of hydrothermal fluid as the main process precipitating the silica. These findings have implications for the range of possible microbial habitats that may develop within chimney structures during their growth, which may include highly variable redox gradients and the availability of different nutrients.