Upper Miocene strata in the Acre sub-basin, Brazil, consist dominantly of various types of inclined heterolithic stratification and pedogenic horizons. These strata were sedimentologically and ichnologically described to: (i) study different temporal controls responsible for inclined heterolithic stratification generation and their variation in a distal–proximal trend; and (ii) delineate the depositional setting. For this purpose, nine representative outcrops were sedimentologically and ichnologically studied, and their facies associations described. Thickness variations of the heterolithic strata of various orders (lamina, lamina bundles and beds) were analysed by statistical methods (Fourier transform). The deposits were interpreted as tidally and seasonally influenced estuarine or delta-related and continental strata. The inclined heterolithic stratification deposits represented vastly different settings ranging from tidally dominated, brackish-water ichnofossils-bearing channels to seasonally controlled, articulated Purussaurus (a freshwater alligator) fossil-bearing channels. Several time cycles were distinguished in the strata, including semi-diurnal, fortnightly and seasonal. Tidal imprint was best observed in low-energy brackish-water settings, whereas seasonal rhythmicity was distinguishable throughout the depositional system. However, the latter was most apparent in riverine channels proximal to the inferred fluvio-tidal transition. The different temporal controls commonly had distinguishable impact on sedimentological and ichnological properties in the studied sediments. The differing properties included: (i) the degree and nature of lateral variability with respect to lithology and bedforms in inclined heterolithic stratification; (ii) the lateral continuity of inclined heterolithic stratification; (iii) the nature of sedimentary contacts between the inclined heterolithic stratification members; (iv) thickness variation of inclined heterolithic stratification members within a set; (v) the cyclicities observed in inclined heterolithic stratification series; (vi) the degree of bioturbation; (vii) the types of trace fossils observed; and (viii) the distribution of bioturbation in adjacent inclined heterolithic stratification members.