The purpose of this pilot study was to identify impact differences in the rehabilitation of balance, gait and functional capacity in patients with lower limb amputation performing hydrokinetic therapy and kinesiotherapy programs during the pre-prosthetic and prosthetic phases. The study included 16 male patients aged 40–60 years with amputated lower limbs for 6 to 12 months, which involved transfemoral amputation (TFA), transtibial amputation (TTA), traumatic and vascular amputation, who were divided into the following two groups: the hydrokinetic therapy (HKT) group and the kinesiotherapy (KT) group, named after the content of the rehabilitation programs that were implemented for 2 weeks in the pre-prosthetic and prosthetic periods. The initial and final evaluation of the participants included the following tests: the Berg Scale and the four square test for the evaluation of the balance; the PodoSmart device for gait assessment; through the walking test over 6 min, we evaluated the functional capacity. The results were processed in SPSS 24. Analysis of the results on balance rehabilitation through the Berg Scale highlighted that the progress related to the mean of the total score was 7.62 points, p = 0.00 for the HKT group and 7.50 points, p = 0.00 for the KT group, while in the four square step test, the mean of progress was 6.125 s, p = 0.00 for the HKT group and 6 s, p = 0.000 for the KT group. The PodoSmart gait analysis revealed that the HKT group showed a progress mean of 4.875%, p = 0.00, for the foot symmetry parameter, which was 1.875% less than the score achieved by the KT group whose symmetry progress mean was 6.75%, p = 0.00, while the average progress mean for the cadence parameter was 2.75 steps/min higher for the KT group than the HKT group. The comparative analysis of the impact of these two programs on the patients’ functional capacity indicated that the score recorded by the KT group was a progress mean of 15.12 m, p = 0.00 better than the HKT group for the travelled distance parameter; the implementation of the hydrokinetic therapy program led to better exercise adaptation for the HKT group compared to the KT group at an average HR (HRavg) with 0.50 BPM, p = 0.00. After analyzing the results, it has been found that hydrokinetic therapy programs have a greater impact on balance rehabilitation and exercise adaptation, while kinesiotherapy programs have a greater impact on gait rehabilitation and functional capacity optimization for the travelled distance parameter.