Would dissolving a salt and letting it sit for 48 hours have an effect on the solution?
The only reactions that I would expect to occur to any significant extent with pure water are acid-base reactions between the citrate and water, where water, being amphiprotic, could act as either an acid or a base:

$$\ce{C6H6O7^2- + H2O &lt;=&gt; C6H7O7- + OH-}$$
$$\ce{C6H6O7^2- + H2O &lt;=&gt; C6H5O7^3- + H3O+}$$

Citrate, being the conjugate base of a weak acid, is itself a weak base (according to the citric acid Wikipedia page, the $\mathrm pK_\mathrm a$ for the dissociation of the second proton is 4.75, and for the third between 5.41 and 6.40). Citrate is tripotic, and in the magnesium salt citrate possesses one undissociated acidic proton, which makes it an amphiprotic molecule as well. Given that the $\mathrm pK_\mathrm a$ of water is approximately 15.7, and the $\mathrm pK_\mathrm a$ of hydronium ($\ce{H3O+}$) is −1.74, both reactions above favor the reactants over the products by many orders of magnitude, though the second reaction is favored above the first (i.e., the dibasic magnesium citrate salt should still be very slightly acidic, overall).

Acid-base reactions typically reach equilibrium quite quickly, so there should be very little change in pH and no pH-attributable differences in taste over time. If any change does occur, I would expect it to be the result of a change in concentration as the water gradually evaporates. Another possibility is that, if the water is impure (which tap water certainly is), additional side-reactions might occur. What those are would depend on the exact composition of the water as well as environmental conditions. It's possible for the magnesium to form a precipitate, for example, in combination with other anions dissolved in the water (unlikely given the quantity in your example, but possible). If the magnesium citrate is part of a commercial product containing other ingredients, then it may well be that other agents are responsible for any effects you observe.