The deposition and nanostructure of polyelectrolyte (PEL) multilayers (PEMs) of branched poly(ethyleneimine)/poly(acrylic acid) (PEI/PAA) onto silicon substrates was studied in terms of the dependence of pH and the PEL concentration (cPEL) in the individual adsorption steps z. Both a commercial automatic dipping device and a homebuilt automatic stream coating device (flow cell) were used. Gravimetry, SFM, transmission (TRANS) and in situ attenuated total reflection (ATR) FTIR spectroscopy were used for the quantitative determination of the adsorbed amount, thickness, chemical composition and morphology of deposited PEMs, respectively. Firstly, the combination of pH = 10 for PEI and pH = 4 for PAA, where both PEL were predominantly in the neutral state, resulted in an extraordinarily high PEM deposition, while pH combinations, where one PEL component was charged, resulted in a significantly lower PEM deposition. This was attributed to both PEL conformation effects and acid/base interactions between basic PEI and acidic PAA. Secondly, for that pH combination an exponential relationship between PEM thickness and adsorption step z was found. Thirdly, based on the results of three independent methods, the course of the deposited amount of a PEM-10 (z = 10) versus cPEL in the range 0.001 to 0.015 M at pH = 10/4 was non-monotonous showing a pronounced maximum at cPEL = 0.005 M. Analogously, for cPEL = 0.005 M a maximum of roughness and structure size was found. Fourthly, related to that finding, in situ ATR-FTIR measurements gave evidence for the release of outermost located PEI upon PAA immersion (even step) and of outermost PAA upon PEI immersion (odd step) under formation of PEL complexes in solution. These studies help us to prepare PEL-based films with a defined thickness and morphology for interaction with biofluids in the biomedical and food fields.