In this work, it was aimed to remove the highly toxic rhodamine B (RhB) dye from wastewater by using a low-cost, renewable, sustainable, and completely natural adsorbent obtained from St. John’s wort (Hypericum perforatum) (HP), which is considered an agro-waste. HP was characterized by FTIR-ATR, XRD, FESEM, and pHpzc. Adsorption experiments were conducted by optimizing pH (2–12), dose (0.01–0.30 g), time (0–120 min), and concentration (10–50 mg/L). Equilibrium data were applied to linear isotherms. The results stated that the removal process occurred in a monolayer on the homogeneous surface of HP and the $${q}_{m}$$
q
m
value was determined as 196.08 mg/g at 298 K. Kinetic results showed that RhB adsorption on HP followed a quasi-second-order. The effect of salt concentration onto RhB adsorption on HP adsorbent and reusability studies were conducted. Thermodynamic tests showed that the process was exothermic ($${\varDelta H}_{A}^{o}=-13.58 kJ/mol$$
Δ
H
A
o
=
-
13.58
k
J
/
m
o
l
) and spontaneous ($${\varDelta G}_{A}^{o}=-26.61 kJ/mol$$
Δ
G
A
o
=
-
26.61
k
J
/
m
o
l
). The results of the study indicated that HP may be a favorable adsorbent for basic dyes in wastewater.
Graphical abstract