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Abstract Single particle resolution is a requirement for numerous experimental protocols that emulate the dynamics of small systems in a bath. Here, we accurately resolve through atom counting the stochastic dynamics of a few sodium atoms in presence of a cold potassium cloud. This capability enables us to rule out the effect of inter-species interaction on sodium atom number dynamics, at very low atomic densities present in these experiments. We study the noise sources for sodium and potassium in a common framework. Thereby, we assign the detection limits to 4.3 atoms for potassium and 0.2 atoms (corresponding to 96% fidelity) for sodium. This opens possibilities for future experiments with a few atoms immersed in a quantum degenerate gas.