diff --git a/devel/py-zarr/Makefile b/devel/py-zarr/Makefile
index 20a10d7b58a6..f90c07636023 100644
--- a/devel/py-zarr/Makefile
+++ b/devel/py-zarr/Makefile
@@ -1,23 +1,26 @@
 PORTNAME=	zarr
-DISTVERSION=	2.18.4
+DISTVERSION=	3.1.3
 CATEGORIES=	devel python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Implementation of chunked, compressed, N-dimensional arrays for Python
-WWW=		https://zarr.readthedocs.io/en/stable/
+WWW=		https://zarr.readthedocs.io/en/stable/ \
+		https://github.com/zarr-developers/zarr-python
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-BUILD_DEPENDS=	${PY_SETUPTOOLS} \
-		${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}asciitree>0:graphics/py-asciitree@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}fasteners>0:devel/py-fasteners@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}numcodecs>=0.10.0:misc/py-numcodecs@${PY_FLAVOR} \
-		${PYNUMPY}
+BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}hatch-vcs>=0:devel/py-hatch-vcs@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}hatchling>=1.27.0:devel/py-hatchling@${PY_FLAVOR}
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}donfig>=0.8:devel/py-donfig@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numcodecs>=0.14:misc/py-numcodecs@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numpy>=1.26,1:math/py-numpy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}packaging>=22.0:devel/py-packaging@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.9:devel/py-typing-extensions@${PY_FLAVOR}
+# numcodecs[crc32c]
+RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}crc32c>=2.7:devel/py-crc32c@${PY_FLAVOR}
 RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}fsspec>0:filesystems/py-fsspec@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR}
 
diff --git a/devel/py-zarr/distinfo b/devel/py-zarr/distinfo
index 26e816e4b201..cc9f73f3cb18 100644
--- a/devel/py-zarr/distinfo
+++ b/devel/py-zarr/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1734080261
-SHA256 (zarr-2.18.4.tar.gz) = 37790ededd0683ae1abe6ff90aa16c22543b3436810060f53d72c15e910c24bb
-SIZE (zarr-2.18.4.tar.gz) = 3603684
+TIMESTAMP = 1760642339
+SHA256 (zarr-3.1.3.tar.gz) = 01342f3e26a02ed5670db608a5576fbdb8d76acb5c280bd2d0082454b1ba6f79
+SIZE (zarr-3.1.3.tar.gz) = 349125
diff --git a/devel/py-zarr/files/patch-pyproject.toml b/devel/py-zarr/files/patch-pyproject.toml
deleted file mode 100644
index 1a3e973ddb61..000000000000
--- a/devel/py-zarr/files/patch-pyproject.toml
+++ /dev/null
@@ -1,9 +0,0 @@
---- pyproject.toml.orig	2024-12-12 16:02:37 UTC
-+++ pyproject.toml
-@@ -1,5 +1,5 @@
- [build-system]
--requires = ["setuptools>=64", "setuptools-scm>8"]
-+requires = ["setuptools", "setuptools-scm>8"]
- build-backend = "setuptools.build_meta"
- 
-