Ultra-small silicon quantum dots (SQD) (< 2 nm diameter) have recently attracted significant interest for a variety of biomedical and optoelectronic applications due to their intriguing optical properties. This work reports the synthesis and detailed photo physical studies of six SQD dyads of 1.8 nm average diameter covalently functionalized by linking to Rhodamine 6G (R6G) and Rhodamine B isothiocyanate (RITC) derivatives through several different spacers. The utilized spacers varied in length, chemical nature, and attachment position with the dyes to produce six different SQD dyads. The photophysical results revealed clear evidence for energy and/or electron transfer with different interaction rates for all dyads. The SQD-RITC dyad family gave enhanced efficiency compared to the SQD/R6G family with a single photoluminescence (PL) peak and complete quenching of the SQDs emission. The SQD/R6G family showed a dual emission peak in which the SQDs PL maxima were blue shifted. This indicates a vital role for the spacers to control the interactions of the ligands with the electronic wave function of SQDs in order to help tune their optical properties. Interestingly, the functionalization of SQDs with dyes extended their photostability for at least sixteen months. The SQDs assemblies were tested for interaction with heavy metal ions (Cu2+, Pb2+, and Ni2+) where results indicated their potential applications as metal sensors in aqueous solutions.