Cross-sectional scanning tunneling microscopy (X-STM) was employed to characterize the InAs submono-layer quantum dots (SMLQDs) grown on top of a Si-doped GaAs(001) substrate in the presence of (2×4) andc(4×4) surface reconstructions. Multiple layers were grown under different conditions to study their effectson the formation, morphology, and local composition of the SMLQDs. The morphological and compositionalvariations in the SMLQDs were observed by both filled and empty-state imaging. A detailed analysis of indiumsegregation in the SMLQD layers was described by fitting the local indium-concentration profile with a standardsegregation model. We observed a strong influence of the arsenic flux over the indium incorporation andformation of the SMLQDs. We investigated the well-width fluctuations of the InGaAs quantum well in which theSMLQDs were formed. The well-width fluctuations were small compared to the more pronounced compositionfluctuations in all the layers. The lateral compositional variations lead to the formation of indium-rich clusterswhich can act as quantum dots and yield charge-carrier confinement.