The continuous supply of land derived organic carbon by rivers is significant to the ocean carbon cycle. In river-estuary systems, the composition and distribution of sedimentary organic matter (OM) can provide detailed information on the balance of land-derived inputs and in situ productivity. This insight is significant for an improved understanding of anthropogenic activity and the changing climate. In the Gulf of Guinea (GoG), high rainfall, coupled with flooding and a warmer climate have direct impacts on OM distributions. Glycerol dialkyl glycerol tetraethers (GDGTs) have been used extensively to investigate OM. In this study, we focused on the widespread occurrence of isoprenoid GDGTs (isoGDGTs), branched GDGTs (brGDGTs), H-tetraethers (H-isoGDGTs and H-brGDGTs), hydroxyl GDGTs (OH-GDGTs), isoGDGT isomers, methylated isoGDGTs (Me-GDGTs), butanetriol and pentanetriol tetraethers (BDGTs and PDGTs), in short sediment cores collected from the inner and outer Qua Iboe River Estuary, located in the GoG. We further determined total organic carbon (Corg), total nitrogen (TN), long chain hydrocarbons (LCA; C27–C33n-alkanes), dinosterol, brassicasterol and phytol, to estimate OM sources, flooding activity, OM degradation, to reconstruct pH and to determine past tropical temperatures. The distribution patterns of GDGTs, use of principal component analysis (PCA), heatmap hierarchical cluster analysis, correlation models, the ratios of isoGDGTs/brGDGTs, ring index (RI), brGDGT-IIIa/IIa, branched and isoprenoid tetraether (BIT), Corg/TN and terrestrial-marine biomarker ratio (TMBR) were all sensitive for indicating terrestrial vs marine OM contributions to the total OM of the tropical estuarine sediments. Marine OM persisted from subsurface to bottom sediment layers (8–38 cm) in the outer estuary site, while a mixed OM source was observed in inner estuary sediments. The Cren/Cren’ ratio >58.5 (up to 83.8), pointed to a predominance of Thaumarchaeota group I.1a microbes. The Methane Index (MI) and isoGDGT-0/Cren ratio indicated significant imprints of a non-methanotrophic archaeal community. A positive linearity of total BDGTs and PDGTs plotted against MI and isoGDGT-0/Cren suggested that these compounds are produced by the same group of the non-methanogenic archaeal community in this tropical estuary. Thus, Methanomassiliicoccus luminyensis is not the only source of BDGTs and PDGTs in the marine environment. Further, the calculated CBT5me derived pH reflected in situ measured sediment pH (6.3). TEX86H-derived sea surface temperature (SST), within error, reflected water column temperature. Calculated brGDGT mean annual air temperatures (MAATs) reflected average annual atmospheric temperatures. Ring index OH-GDGTs temperature proxies (RI-OH SSTsummer and RI-OHꞌ SST) reflected mean dry season (November to February) temperatures. A newly derived MAAT proxy, calculated from H-brGDGT, also reflected the tropical annual air temperature (23–28 °C). Altogether, as expected, the OM sources are traced largely to both terrestrial and marine inputs. The terrestrial OM was deposited by excess flooding and surface runoff occasioned by torrential monsoon rains in recent years, triggered by climate change, while mesotidal currents introduced marine OM into the Qua Iboe River Estuary system. This study further contributes to our understanding of OM distributions in warmer climate conditions.