[bobo.gardener]

I have encountered with problem when trying to calculate concentration of malic acid from known pH = 3,9(c=0.000125 M) considering only first degree of dis, so pKa=3,4(Ka=0.000398). Think that bothers me is  calculated concentration of malic acid is 3.9*10^-5.
by formula Ka=([H+]*[A-])/[HA] i derived it so: [HA]=([H+]*[A-])/Ka

in numbers :  [HA]= (0.000125 * 0.000125)/0.000398
                   [HA]=0.000039

I have bad feeling, that my calculations or understanding of this topic is flawed, but how can concentration of acid before dissociation be lower than actual concentration of its ions?

[AWK]

Use different approximation
Ka=[H₃O⁺]²/(c-[H₃O⁺])

[Borek]

You have calculated concentration of HA - but that's not the analytical concentration of the acid. What about the dissociation product, A^-?