Context. With the outstanding spatial resolution and sensitivity of the Atacama Large Millimeter/sub-millimeter Array (ALMA), molecular gas other than the abundant CO can be observed and resolved in circumstellar envelopes (CSEs) around evolved stars, such as the binary S-type asymptotic giant branch (AGB) star W Aquilae. Aims. We aim to constrain the chemical composition of the CSE and determine the radial abundance distribution, the photospheric peak abundance, and isotopic ratios of a selection of chemically important molecular species in the innermost CSE of W Aql. The derived parameters are put into the context of the chemical evolution of AGB stars and are compared with theoretical models. Methods. We employ one-dimensional radiative transfer modeling – with the accelerated lambda iteration (ALI) radiative transfer code–of the radial abundance distribution of a total of five molecular species (CS, SiS, ³⁰SiS, ²⁹SiO and H¹³CN) and determine the best fitting model parameters based on high-resolution ALMA observations as well as archival single-dish observations. The additional advantage of the spatially resolved ALMA observations is that we can directly constrain the radial profile of the observed line transitions from the observations. Results. We derive abundances and e-folding radii for CS, SiS, ³⁰SiS, ²⁹SiO and H¹³CN and compare them to previous studies, which are based only on unresolved single-dish spectra. Our results are in line with previous results and are more accurate due to resolution of the emission regions.